Simian adenovirus nucleic acid and amino acid sequences, vectors containing same, and methods of use

ABSTRACT

A recombinant vector comprises simian adenovirus sequences and a heterologous gene under the control of regulatory sequences. A cell line which expresses simian adenovirus gene(s) is also disclosed. Methods of using the vectors and cell lines are provided.

INCORPORATION-BY-REFERENCE OF MATERIAL SUBMITTED IN ELECTRONIC FORM

Applicant hereby incorporates by reference the Sequence Listing materialfiled in electronic form herewith. This file is labeled“O2677C4_Sequence_ST25.txt”.

BACKGROUND OF THE INVENTION

Adenovirus is a double-stranded DNA virus with a genome size of about 36kilobases (kb), which has been widely used for gene transferapplications due to its ability to achieve highly efficient genetransfer in a variety of target tissues and large transgene capacity.Conventionally, E1 genes of adenovirus are deleted and replaced with atransgene cassette consisting of the promoter of choice, cDNA sequenceof the gene of interest and a poly A signal, resulting in a replicationdefective recombinant virus.

Adenoviruses have a characteristic morphology with an icosahedral capsidconsisting of three major proteins, hexon (II), penton base (III) and aknobbed fibre (IV), along with a number of other minor proteins, VI,VIII, IX, IIIa and IVa2 [W. C. Russell, J. Gen Virol., 81:2573-2604(November 2000)]. The virus genome is a linear, double-stranded DNA witha terminal protein attached covalently to the 5′ termini, which haveinverted terminal repeats (ITRs). The virus DNA is intimately associatedwith the highly basic protein VII and a small peptide termed mu. Anotherprotein, V, is packaged with this DNA-protein complex and provides astructural link to the capsid via protein VI. The virus also contains avirus-encoded protease, which is necessary for processing of some of thestructural proteins to produce mature infectious virus.

Recombinant adenoviruses have been described for delivery of moleculesto host cells. See, U.S. Pat. No. 6,083,716, which describes the genomeof two chimpanzee adenoviruses.

What is needed in the art are more effective vectors which avoid theeffect of pre-existing immunity to selected adenovirus serotypes in thepopulation and/or which are useful for repeat administration and fortiter boosting by second vaccination, if required.

SUMMARY OF THE INVENTION

The present invention provides the isolated nucleic acid sequences andamino acid sequences of six simian adenoviruses, vectors containingthese sequences, and cell lines expressing simian adenovirus genes. Alsoprovided are a number of methods for using the vectors and cells of theinvention.

The methods of the invention involve delivering one or more selectedheterologous gene(s) to a mammalian patient by administering a vector ofthe invention. Because the various vector constructs are derived fromsimian rather than from human adenoviruses, the immune system of thenon-simian human or veterinary patient is not primed to respondimmediately to the vector as a foreign antigen. Use of the compositionsof this invention thus permits a more stable expression of the selectedtransgene when administered to a non-simian patient. Use of thecompositions of this invention for vaccination permits presentation of aselected antigen for the elicitation of protective immune responses.Without wishing to be bound by theory, the ability of the adenovirusesof the invention to transduce human dendritic cells is at leastpartially responsible for the ability of the recombinant constructs ofthe invention to induce an immune response. The recombinant simianadenoviruses of this invention may also be used for producingheterologous gene products in vitro. Such gene products are themselvesuseful in a variety for a variety of purposes such as are describedherein.

These and other embodiments and advantages of the invention aredescribed in more detail below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 provides an alignment of the amino acid sequences of the L1 and aportion of the L2 loops of the capsid protein hexon of the chimpanzeeadenovirus C1 [SEQ ID NO:13], chimpanzee adenovirus C68 (Pan-9) [SEQ IDNO:14], and the novel Pan5 [SEQ ID NO:15], Pan6 [SEQ ID NO: 16] and Pan7[SEQ ID NO: 17] chimpanzee adenovirus sequences of the invention. Theintervening conserved region is part of the pedestal domain conservedbetween adenovirus serotypes.

FIG. 2 provides an alignment of the amino acid sequences of the fiberknob domains of chimpanzee C68 (Pan-9) [SEQ ID NO:18], Pan-6 [SEQ IDNO:19], Pan-7 [SEQ ID NO:20], and Pan-5 [SEQ ID NO:21] and the humanadenoviruses serotypes 2 [SEQ ID NO:22] and 5 [SEQ ID NO:23].

DETAILED DESCRIPTION OF THE INVENTION

The invention provides novel nucleic acid and amino acid sequences fromAd Pan5 [SEQ ID NO:1-4, 15 and 21], Ad Pan6 [SEQ ID NO: 5-8, 16, 19],and Ad serotype Pan7 [SEQ ID NO: 9-12, 17, 20], which were originallyisolated from chimpanzee lymph nodes. In several instances throughoutthe specification, these adenoviruses are alternatively termed hereinC5, C6 and C7, respectively. Also provided are sequences from adenovirusSV1 [SEQ ID NO: 24-28], which was originally isolated from the kidneycells of cynomolgus monkey. The invention also provides sequences ofadenoviruses SV-25 [SEQ ID NO:29-33] and SV-39 [SEQ ID NO: 34-37], whichwere originally isolated from rhesus monkey kidney cells.

The present invention provides novel adenovirus vectors and packagingcell lines to produce those vectors for use in the in vitro productionof recombinant proteins or fragments or other reagents. The inventionfurther provides compositions for use in delivering a heterologousmolecule for therapeutic or vaccine purposes. Such therapeutic orvaccine compositions contain the adenoviral vectors carrying an insertedheterologous molecule. In addition, novel sequences of the invention areuseful in providing the essential helper functions required forproduction of recombinant adeno-associated viral (AAV) vectors. Thus,the invention provides helper constructs, methods and cell lines whichuse these sequences in such production methods.

The term “substantial homology” or “substantial similarity,” whenreferring to a nucleic acid or fragment thereof, indicates that, whenoptimally aligned with appropriate nucleotide insertions or deletionswith another nucleic acid (or its complementary strand), there isnucleotide sequence identity in at least about 95 to 99% of the alignedsequences.

The term “substantial homology” or “substantial similarity,” whenreferring to amino acids or fragments thereof, indicates that, whenoptimally aligned with appropriate amino acid insertions or deletionswith another amino acid (or its complementary strand), there is aminoacid sequence identity in at least about 95 to 99% of the alignedsequences. Preferably, the homology is over full-length sequence, or aprotein thereof, or a fragment thereof which is at least 8 amino acids,or more desirably, at least 15 amino acids in length. Examples ofsuitable fragments are described herein.

The term “percent sequence identity” or “identical” in the context ofnucleic acid sequences refers to the residues in the two sequences thatare the same when aligned for maximum correspondence. The length ofsequence identity comparison may be over the full-length of the genome(e.g., about 36 kbp), the full-length of an open reading frame of agene, protein, subunit, or enzyme [see, e.g., the tables providing theadenoviral coding regions], or a fragment of at least about 500 to 5000nucleotides, is desired. However, identity among smaller fragments, e.g.of at least about nine nucleotides, usually at least about 20 to 24nucleotides, at least about 28 to 32 nucleotides, at least about 36 ormore nucleotides, may also be desired. Similarly, “percent sequenceidentity” may be readily determined for amino acid sequences, over thefull-length of a protein, or a fragment thereof. Suitably, a fragment isat least about 8 amino acids in length, and may be up to about 700 aminoacids. Examples of suitable fragments are described herein.

Identity is readily determined using such algorithms and computerprograms as are defined herein at default settings. Preferably, suchidentity is over the full length of the protein, enzyme, subunit, orover a fragment of at least about 8 amino acids in length. However,identity may be based upon shorter regions, where suited to the use towhich the identical gene product is being put.

As described herein, alignments are performed using any of a variety ofpublicly or commercially available Multiple Sequence Alignment Programs,such as “Clustal W”, accessible through Web Servers on the internet.Alternatively, Vector NTI utilities are also used. There are also anumber of algorithms known in the art that can be used to measurenucleotide sequence identity, including those contained in the programsdescribed above. As another example, polynucleotide sequences can becompared using Fasta, a program in GCG Version 6.1. Fasta providesalignments and percent sequence identity of the regions of the bestoverlap between the query and search sequences. For instance, percentsequence identity between nucleic acid sequences can be determined usingFasta with its default parameters (a word size of 6 and the NOPAM factorfor the scoring matrix) as provided in GCG Version 6.1, hereinincorporated by reference. Similarly programs are available forperforming amino acid alignments. Generally, these programs are used atdefault settings, although one of skill in the art can alter thesesettings as needed. Alternatively, one of skill in the art can utilizeanother algorithm or computer program that provides at least the levelof identity or alignment as that provided by the referenced algorithmsand programs.

As used throughout this specification and the claims, the term“comprise” and its variants including, “comprises”, “comprising”, amongother variants, is inclusive of other components, elements, integers,steps and the like. The term “consists of” or “consisting of” areexclusive of other components, elements, integers, steps and the like.

I. The Simian Adenovirus Sequences

The invention provides nucleic acid sequences and amino acid sequencesof Pan5, Pan6, Pan7, SV1, SV25 and SV39, which are isolated from theother viral material with which they are associated in nature.

A. Nucleic Acid Sequences

The Pan5 nucleic acid sequences of the invention include nucleotides 1to 36462 of SEQ ID NO:1. The Pan6 nucleic acid sequences of theinvention include nucleotides 1 to 36604 of SEQ ID NO: 5. The Pan7nucleic acid sequences of the invention include nucleotides 1 to 36535of SEQ ID NO: 9. The SV1 nucleic acid sequences of the invention includenucleotides 1 to 34264 of SEQ ID NO: 24. The SV25 nucleic acid sequencesof the invention include nucleotides 1 to 31044 of SEQ ID NO: 29. TheSV39 nucleic acid sequences of the invention include nucleotides 1 to34115 of SEQ ID NO: 34. See, Sequence Listing, which is incorporated byreference herein.

The nucleic acid sequences of the invention further encompass the strandwhich is complementary to the sequences of SEQ ID NO: 5, 9, 24, 29 and34, as well as the RNA and cDNA sequences corresponding to the sequencesof these sequences figures and their complementary strands. Furtherincluded in this invention are nucleic acid sequences which are greaterthan 95 to 98%, and more preferably about 99 to 99.9% homologous oridentical to the Sequence Listing. Also included in the nucleic acidsequences of the invention are natural variants and engineeredmodifications of the sequences provided in SEQ ID NO: 5, 9, 24, 29 and34 and their complementary strands. Such modifications include, forexample, labels that are known in the art, methylation, and substitutionof one or more of the naturally occurring nucleotides with a degeneratenucleotide.

The invention further encompasses fragments of the sequences of Pan5,Pan6, Pan7, SV1, SV25 and SV39, their complementary strand, cDNA and RNAcomplementary thereto. Suitable fragments are at least 15 nucleotides inlength, and encompass functional fragments, i.e., fragments which are ofbiological interest. For example, a functional fragment can express adesired adenoviral product or may be useful in production of recombinantviral vectors. Such fragments include the gene sequences and fragmentslisted in the tables below.

The following tables provide the transcript regions and open readingframes in the simian adenovirus sequences of the invention. For certaingenes, the transcripts and open reading frames (ORFs) are located on thestrand complementary to that presented in SEQ ID NO: 5, 9, 24, 29 and34. See, e.g., E2b, E4 and E2a. The calculated molecular weights of theencoded proteins are also shown. Note that the E1a open reading framePan5 [nt 576-1436 of SEQ ID NO:1], Pan6 [nt 576 to 1437 of SEQ ID NO: 5]and Pan7 [nt 576 to 1437 of SEQ ID NO: 9] contain internal splice sites.These splice sites are noted in the following tables.

Ad Pan-5 [SEQ ID NO: 1] Start End M. W. Regions (nt) (nt) (Daltons) ITR1 120 — E1a Transcript 478 — 13S 576-664, 1233- 28120 1436 12S 576-1046,1233- 24389 1436 9S 576-644, 1233- 9962 1436 Transcript 1516 — E1bTranscript 1552 — Small T 1599 2171 22317 Large T 1904 3412 55595 IX3492 3920 14427 Transcript 3959 E2b Transcript 10349 — PTP 10349 845172930 Polymerase 8448 5083 127237 IVa2 5604 3980 50466 Transcript 396028.1 kD 5155 5979 28141 Agnoprotein 7864 8580 25755 L1 Transcript 10849— 52/55D 10851 12025 IIIa 12050 13819 65669 Transcript 13832 —Transcript 13894 — L2 Penton 13898 15490 59292 VII 15494 16078 21478 V16123 17166 39568 Mu 17189 17422 8524 transcript 17442 — Transcript17488 — L3 VI 17491 18222 26192 Hexon 18315 21116 104874 Endoprotease20989 21783 28304 transcript 21811 — E2a Transcript 26782 — DBP 2338621845 57358 transcript 21788 — L4 Transcript 23406 — 100 kD 23412 2580588223 33 kD homolog 25525 26356 24538 VIII 26428 27111 24768 transcript27421 — E3 Transcript 26788 — Orf #1 27112 27432 12098 Orf #2 2738628012 23040 Orf #3 27994 28527 19525 Orf #4 28557 29156 22567 Orf #529169 29783 22267 Orf #6 29798 30673 31458 Orf #7 30681 30956 10477 Orf#8 30962 31396 16523 Orf #9 31389 31796 15236 transcript 31837 — L5Transcript 32032 — Fiber 32035 33372 47670 transcript 33443 — E4Transcript 36135 — Orf 7 33710 33462 9191 Orf 6 34615 33710 35005 Orf 434886 34521 13878 Orf 3 35249 34896 13641 Orf 2 35635 35246 14584 Orf 136050 35676 13772 Transcript 33437 — ITR 36343 36462 —

Ad Pan-6 [SEQ ID NO: 5] End M. W. Regions Start (nt) (nt) (Daltons) ITR1 123 — E1a transcript 478 — 13S 576-1143, 1229- 28291 1437 12S576-1050, 1229- 24634 1437 9S 576-645, 1229- 10102 1437 transcript 1516— E1b transcript 1553 — Small T 1600 2172 22315 LargeT 1905 3413 55594IX 3498 3926 14427 transcript 3965 — E2b transcript 10341 — PTP 103408451 72570 Polymerase 8445 5089 126907 IVa2 5610 3986 50452 transcript3966 — L1 transcript 10838 — 52/55 kD 10840 12012 44205 IIIa 12036 1379965460 Transcript 13812 — 28.1 kd 5161 5985 28012 Agnoprotein 7870 858025382 L2 transcript 13874 — Penton 13878 15467 59314 VII 15471 1605521508 V 16100 17137 39388 Mu 17160 17393 8506 transcript 17415 — L3transcript 17466 — VI 17469 18188 25860 Hexon 18284 21112 106132Endoprotease 21134 21754 23445 transcript 21803 — E2a transcript 26780 —DBP 23375 21837 57299 transcript 21780 — L4 Transcript 23398 — 100 kD23404 25806 88577 33 kD homolog 25523 26357 24609 VIII 26426 27109 24749transcript 27419 — E3 transcript 26786 — Orf #1 27110 27430 12098 Orf #227384 28007 22880 Orf #3 27989 28519 19460 Orf #4 28553 29236 25403 Orf#5 29249 29860 22350 Orf #6 29875 30741 31028 Orf #7 30749 31024 10469Orf #8 31030 31464 16540 Orf #9 31457 31864 15264 transcript 31907 — L5transcript 32159 — Fiber 32162 33493 47364 transcript 33574 — E4transcript 36276 — Orf 7 33841 33593 9177 Orf 6 34746 33841 35094 Orf 435017 34652 13937 Orf 3 35380 35027 13627 Orf 2 35766 35377 14727 Orf 136181 35807 13739 transcript 33558 — ITR 36482 36604 —

Ad Pan-7 [SEQ ID NO: 9] M. W. Regions Start (nt) End (nt) (Daltons) ITR1 132 — E1a transcript 478 — 13S 576-1143, 1229-1437 28218 12S 576-1050,1229- 1437 24561 9S 576-645, 1229-1437 10102 transcript 1516 — E1btranscript 1553 — Small T 1600 2178 22559 LargeT 1905 3419 55698 IVa23992 5616 50210 transcript 3971 — E2b transcript 10341 — PTP 10340 845772297 Polymerase 8451 5095 126994 IX 3504 3932 14441 transcript 3972 —28.1 kD 5167 5991 28028 Agnoprotein 7876 8586 25424 L1 transcript 1083452/55 kD 10836 12011 44302 IIIa 12035 13795 65339 transcript 13808 — L2transcript 13870 — Penton 13874 15469 59494 VII 15473 16057 21339 V16102 17139 39414 Mu 17167 17400 8506 transcript 17420 — L3 transcript17467 — VI 17470 18198 26105 Hexon 18288 21086 104763 Endoprotease 2110621732 23620 transcript 21781 — E2a transcript 26764 — DBP 23353 2181557199 transcript 21755 — L4 transcript 23370 — 100 kD 23376 25781 8852033 kD 25489 26338 25155 homolog VIII 26410 27093 24749 transcript 27403— E3 transcript 26770 — Orf #1 27094 27414 12056 Orf #2 27368 2798822667 Orf #3 27970 28500 19462 Orf #4 28530 29150 22999 Orf #5 2916329777 22224 Orf #6 29792 30679 32153 Orf #7 30687 30962 10511 Orf #830968 31399 16388 Orf #9 31392 31799 15205 transcript 31842 — L5transcript 32091 — Fiber 32094 33425 47344 transcript 33517 — E4transcript 36208 — Orf 7 33784 33536 9191 Orf 6 34689 33784 35063 Orf 434960 34595 13879 Orf 3 35323 34970 13641 Orf 2 35709 35320 14644 Orf 136123 35749 13746 transcript 33501 — ITR 36404 36535 —

Ad SV-1 Ad SV-25 Ad SV-39 [SEQ ID NO: 24] [SEQ ID NO: 29] [SEQ ID NO:34] Region Start End Start End Start End ITR 1 106 1 133 1 150 E1a 3521120 — — 404 1409 E1b 1301 2891 359 2273 1518 3877 E2b 9257 2882 90872754 10143 3868 E2a 24415 20281 24034 20086 25381 21228 E3 24974 2788624791 25792 25790 29335 E4 33498 30881 30696 28163 33896 31157 ITR 3414534264 30912 31044 33966 34115 ITR 1 106 1 133 1 150 L1 9513 12376 934312206 10416 13383 L2 12453 15858 12283 15696 13444 16877 L3 15910 2027015748 20080 17783 21192 L4 21715 25603 21526 25420 22659 26427 L5 2805930899 25320 28172 29513 31170 ITR 34145 34264 30912 31044 33966 34115

Ad SV-1, SEQ ID NO: 24 protein Start End M. W. ITR 1 106 — E1a 13S 459953 18039 12S E1b Small T LargeT 1301 2413 42293 IX 2391 2885 16882 E2bIVa2 4354 2924 54087 Polymerase 6750 4027 102883 PTP 9257 7371 72413Agno-protein 6850 7455 20984 L1 52/55 kD 9515 10642 42675 IIIa 1066312372 636568 L2 Penton 12454 13965 56725 VII 13968 14531 20397 V 1458815625 39374 Mu 15645 15857 7568 L3 VI 15911 16753 30418 Hexon 1684119636 104494 Endoprotease 19645 20262 23407 2a DBP 21700 20312 52107 L4100 kD 21721 24009 85508 VIII 24591 25292 25390 E3 Orf #1 25292 2560911950 Orf #2 25563 26081 18940 Orf #3 26084 26893 30452 Orf #4 2690827180 10232 Orf #5 27177 17512 12640 Orf #6 27505 27873 13639 L5 Fiber#2 28059 29150 39472 Fiber #1 29183 30867 61128 E4 Orf 7 31098 308927837 Orf 6 31982 31122 33921 Orf 4 32277 31915 14338 Orf 3 32629 3227913386 Orf 2 33018 32626 14753 Orf 1 33423 33043 14301 ITR 34145 34264

Ad SV-25, Ad SV-39, SEQ ID NO: 29 SEQ ID NO: 34 protein Start End M. W.Start End M. W. ITR 1 133 — 1 150 — E1a 13S 492 1355 28585 12S 492 135525003 E1b Small T 478 1030 20274 1518 2075 21652 Large T 829 2244 523101823 3349 55534 IX 2306 2716 13854 3434 3844 14075 E2b IVa2 4208 275554675 3912 5141 46164 Poly- 6581 3858 102839 7753 5033 103988 merase PTP9087 7207 71326 10143 8335 69274 Agno- 6681 7139 16025 — — — protein L152/55 kD 9345 10472 42703 10418 11608 44232 IIIa 10493 12202 63598 1157413364 66078 L2 Penton 12284 13801 56949 13448 14959 56292 VII 1380614369 20369 14960 15517 20374 V 14426 15463 39289 15567 16628 39676 Mu15483 15695 7598 16650 16871 7497 L3 VI 15749 16591 30347 16925 1769528043 Hexon 16681 19446 104035 17785 20538 102579 Endo- 19455 2007223338 20573 21181 22716 protease 2a DBP 21511 20123 52189 22631 2123153160 L4 100 kD 21532 23829 85970 22659 25355 100362 VIII 24408 2510925347 25410 26108 25229 E3 Orf #1 25109 25426 11890 26375 27484 42257Orf #2 27580 28357 29785 Orf #3 28370 28645 10514 Orf #4 28863 2933318835 Orf #5 Orf #6 L5 Fiber #2 25380 26423 37529 Fiber #1 26457 2813660707 29515 31116 56382 E4 Orf 7 31441 31118 11856 Orf 6 29255 2839533905 32292 31438 33437 Orf 4 29550 29188 14399 32587 32222 13997 Orf 329902 29552 13284 32954 32607 13353 Orf 2 30291 29899 14853 33348 3295914821 Orf 1 30316 30696 14301 33764 33378 14235 ITR 30912 31044 3396634115

The Pan5, Pan6, Pan7, SV1, SV25 and SV39 adenoviral nucleic acidsequences are useful as therapeutic agents and in construction of avariety of vector systems and host cells. As used herein, a vectorincludes any suitable nucleic acid molecule including, naked DNA, aplasmid, a virus, a cosmid, or an episome. These sequences and productsmay be used alone or in combination with other adenoviral sequences orfragments, or in combination with elements from other adenoviral ornon-adenoviral sequences. The adenoviral sequences of the invention arealso useful as antisense delivery vectors, gene therapy vectors, orvaccine vectors. Thus, the invention further provides nucleic acidmolecules, gene delivery vectors, and host cells which contain the Adsequences of the invention.

For example, the invention encompasses a nucleic acid moleculecontaining simian Ad ITR sequences of the invention. In another example,the invention provides a nucleic acid molecule containing simian Adsequences of the invention encoding a desired Ad gene product. Stillother nucleic acid molecule constructed using the sequences of theinvention will be readily apparent to one of skill in the art, in viewof the information provided herein.

In one embodiment, the simian Ad gene regions identified herein may beused in a variety of vectors for delivery of a heterologous molecule toa cell. For example, vectors are generated for expression of anadenoviral capsid protein (or fragment thereof) for purposes ofgenerating a viral vector in a packaging host cell. Such vectors may bedesigned for expression in trans. Alternatively, such vectors aredesigned to provide cells which stably contain sequences which expressdesired adenoviral functions, e.g., one or more of E1a, E1b, theterminal repeat sequences, E2a, E2b, E4, E4ORF6 region.

In addition, the adenoviral gene sequences and fragments thereof areuseful for providing the helper functions necessary for production ofhelper-dependent viruses (e.g., adenoviral vectors deleted of essentialfunctions or adeno-associated viruses (AAV)). For such productionmethods, the simian adenoviral sequences of the invention are utilizedin such a method in a manner similar to those described for the humanAd. However, due to the differences in sequences between the simianadenoviral sequences of the invention and those of human Ad, the use ofthe sequences of the invention essentially eliminate the possibility ofhomologous recombination with helper functions in a host cell carryinghuman Ad E1 functions, e.g., 293 cells, which may produce infectiousadenoviral contaminants during rAAV production.

Methods of producing rAAV using adenoviral helper functions have beendescribed at length in the literature with human adenoviral serotypes.See, e.g., U.S. Pat. No. 6,258,595 and the references cited therein.See, also, U.S. Pat. No. 5,871,982; WO 99/14354; WO 99/15685; WO99/47691. These methods may also be used in production of non-humanserotype AAV, including non-human primate AAV serotypes. The simianadenoviral gene sequences of the invention which provide the necessaryhelper functions (e.g., E1a, E1b, E2a and/or E4 ORF6) can beparticularly useful in providing the necessary adenoviral function whileminimizing or eliminating the possibility of recombination with anyother adenoviruses present in the rAAV-packaging cell which aretypically of human origin. Thus, selected genes or open reading framesof the adenoviral sequences of the invention may be utilized in theserAAV production methods.

Alternatively, recombinant adenoviral simian vectors of the inventionmay be utilized in these methods. Such recombinant adenoviral simianvectors may include, e.g., a hybrid chimp Ad/AAV in which chimp Adsequences flank a rAAV expression cassette composed of, e.g., AAV 3′and/or 5′ ITRs and a transgene under the control of regulatory sequenceswhich control its expression. One of skill in the art will recognizethat still other simian adenoviral vectors and/or gene sequences of theinvention will be useful for production of rAAV and other virusesdependent upon adenoviral helper.

In still another embodiment, nucleic acid molecules are designed fordelivery and expression of selected adenoviral gene products in a hostcell to achieve a desired physiologic effect. For example, a nucleicacid molecule containing sequences encoding an adenovirus E1a protein ofthe invention may be delivered to a subject for use as a cancertherapeutic. Optionally, such a molecule is formulated in a lipid-basedcarrier and preferentially targets cancer cells. Such a formulation maybe combined with other cancer therapeutics (e.g., cisplatin, taxol, orthe like). Still other uses for the adenoviral sequences provided hereinwill be readily apparent to one of skill in the art.

In addition, one of skill in the art will readily understand that the Adsequences of the invention can be readily adapted for use for a varietyof viral and non-viral vector systems for in vitro, ex vivo or in vivodelivery of therapeutic and immunogenic molecules. For example, thePan5, Pan6, Pan7, SV1, SV25 and/or SV39 simian Ad genomes of theinvention can be utilized in a variety of rAd and non-rAd vectorsystems. Such vectors systems may include, e.g., plasmids, lentiviruses,retroviruses, poxviruses, vaccinia viruses, and adeno-associated viralsystems, among others. Selection of these vector systems is not alimitation of the present invention.

The invention further provides molecules useful for production of thesimian and simian-derived proteins of the invention. Such moleculeswhich carry polynucleotides including the simian Ad DNA sequences of theinvention can be in the form of naked DNA, a plasmid, a virus or anyother genetic element.

B. Simian Adenoviral Proteins of the Invention

The invention further provides gene products of the above adenoviruses,such as proteins, enzymes, and fragments thereof, which are encoded bythe adenoviral nucleic acids of the invention. The invention furtherencompasses Pan5, Pan6 and Pan7, SV1, SV25 and SV39 proteins, enzymes,and fragments thereof, having the amino acid sequences encoded by thesenucleic acid sequences which are generated by other methods. Suchproteins include those encoded by the open reading frames identified inthe tables above, in FIGS. 1 and 2, and fragments thereof.

Thus, in one aspect, the invention provides unique simian adenoviralproteins which are substantially pure, i.e., are free of other viral andproteinaceous proteins. Preferably, these proteins are at least 10%homogeneous, more preferably 60% homogeneous, and most preferably 95%homogeneous.

In one embodiment, the invention provides unique simian-derived capsidproteins. As used herein, a simian-derived capsid protein includes anyadenoviral capsid protein that contains a Pan5, Pan6, Pan7, SV1, SV25 orSV39 capsid protein or a fragment thereof, as defined above, including,without limitation, chimeric capsid proteins, fusion proteins,artificial capsid proteins, synthetic capsid proteins, and recombinantlycapsid proteins, without limitation to means of generating theseproteins.

Suitably, these simian-derived capsid proteins contain one or more Pan5,Pan6, Pan7, SV1, SV25 or SV39 regions or fragments thereof (e.g., ahexon, penton, fiber or fragment thereof) in combination with capsidregions or fragments thereof of different adenoviral serotypes, ormodified simian capsid proteins or fragments, as described herein. A“modification of a capsid protein associated with altered tropism” asused herein includes an altered capsid protein, i.e, a penton, hexon orfiber protein region, or fragment thereof, such as the knob domain ofthe fiber region, or a polynucleotide encoding same, such thatspecificity is altered. The simian-derived capsid may be constructedwith one or more of the simian Ad of the invention or another Adserotypes which may be of human or non-human origin. Such Ad may beobtained from a variety of sources including the ATCC, commercial andacademic sources, or the sequences of the Ad may be obtained fromGenBank or other suitable sources.

The amino acid sequences of the simian adenoviruses penton proteins ofthe invention are provided herein. The AdPan5 penton protein is providedin SEQ ID NO:2. The AdPan7 penton is provided in SEQ ID NO:6. The AdPan6penton is provided in SEQ ID NO:10. The SV1 penton is provided in SEQ IDNO:25. The SV25 penton protein is provided in SEQ ID NO:30. The SV39penton is provided in SEQ ID NO:35. Suitably, any of these pentonproteins, or unique fragments thereof, may be utilized for a variety ofpurposes. Examples of suitable fragments include the penton havingN-terminal and/or C-terminal truncations of about 50, 100, 150, or 200amino acids, based upon the amino acid numbering provided above and inSEQ ID NO:2; SEQ ID NO:6; SEQ ID NO:25; SEQ ID NO:30, or SEQ ID NO:35.Other suitable fragments include shorter internal, C-terminal, orN-terminal fragments. Further, the penton protein may be modified for avariety of purposes known to those of skill in the art.

The invention further provides the amino acid sequences of the hexonprotein of Pan5 [SEQ ID NO:3], Pan6 [SEQ ID NO:7], Pan 7 [SEQ ID NO:11],SV1 [SEQ ID NO:26], SV25 [SEQ ID NO:31], and/or SV39 [SEQ ID NO:36].Suitably, this hexon protein, or unique fragments thereof, may beutilized for a variety of purposes. Examples of suitable fragmentsinclude the hexon having N-terminal and/or C-terminal truncations ofabout 50, 100, 150, 200, 300, 400, or 500 amino acids, based upon theamino acid numbering provided above and in SEQ ID NO: 3, 7, 11, 26, 31and 36. Other suitable fragments include shorter internal, C-terminal,or N-terminal fragments. For example, one suitable fragment the loopregion (domain) of the hexon protein, designated DE1 and FG1, or ahypervariable region thereof. Such fragments include the regionsspanning amino acid residues about 125 to 443; about 138 to 441, orsmaller fragments, such as those spanning about residue 138 to residue163; about 170 to about 176; about 195 to about 203; about 233 to about246; about 253 to about 264; about 287 to about 297; and about 404 toabout 430 of the simian hexon proteins, with reference to SEQ ID NO: 3,7, 11, 26, 31 or 36. Other suitable fragments may be readily identifiedby one of skill in the art. Further, the hexon protein may be modifiedfor a variety of purposes known to those of skill in the art. Becausethe hexon protein is the determinant for serotype of an adenovirus, suchartificial hexon proteins would result in adenoviruses having artificialserotypes. Other artificial capsid proteins can also be constructedusing the chimp Ad penton sequences and/or fiber sequences of theinvention and/or fragments thereof.

In one example, it may be desirable to generate an adenovirus having analtered hexon protein utilizing the sequences of a hexon protein of theinvention. One suitable method for altering hexon proteins is describedin U.S. Pat. No. 5,922,315, which is incorporated by reference. In thismethod, at least one loop region of the adenovirus hexon is changed withat least one loop region of another adenovirus serotype. Thus, at leastone loop region of such an altered adenovirus hexon protein is a simianAd hexon loop region of the invention (e.g. Pan7). In one embodiment, aloop region of the Pan7 hexon protein is replaced by a loop region fromanother adenovirus serotype. In another embodiment, the loop region ofthe Pan7 hexon is used to replace a loop region from another adenovirusserotype. Suitable adenovirus serotypes may be readily selected fromamong human and non-human serotypes, as described herein. Pan7 isselected for purposes of illustration only; the other simian Ad hexonproteins of the invention may be similarly altered, or used to alteranother Ad hexon. The selection of a suitable serotype is not alimitation of the present invention. Still other uses for the hexonprotein sequences of the invention will be readily apparent to those ofskill in the art.

The invention further encompasses the fiber proteins of the simianadenoviruses of the invention. The fiber protein of AdPan 5 has theamino acid sequence of SEQ ID NO:4. The fiber protein AdPan6 has theamino acid sequence of SEQ ID NO: 8. The fiber protein of AdPan7 has theamino acid sequence of SEQ ID NO: 12. SV-1 has two fiber proteins; fiber2 has the amino acid sequence of SEQ ID NO:27 and fiber 1 has the aminoacid sequence of SEQ ID NO:28. SV-25 also has two fiber proteins; fiber2 has the amino acid sequence of SEQ ID NO:32 and fiber 1 has the aminoacid sequence of SEQ ID NO:33. The fiber protein of SV-39 has the aminoacid sequence of SEQ ID NO:37.

Suitably, this fiber protein, or unique fragments thereof, may beutilized for a variety of purposes. One suitable fragment is the fiberknob, which spans about amino acids 247 to 425 of SEQ ID NO: 4, 8, 12,28, 32, 33 and 37. See FIG. 2. Examples of other suitable fragmentsinclude the fiber having N-terminal and/or C-terminal truncations ofabout 50, 100, 150, or 200 amino acids, based upon the amino acidnumbering provided above and in SEQ ID NO: 4, 8, 12, 28, 32, 33 and 37.Still other suitable fragments include internal fragments. Further, thefiber protein may be modified using a variety of techniques known tothose of skill in the art.

The invention further encompasses unique fragments of the proteins ofthe invention which are at least 8 amino acids in length. However,fragments of other desired lengths can be readily utilized. In addition,the invention encompasses such modifications as may be introduced toenhance yield and/or expression of a Pan5, Pan6, Pan7, SV1, SV25 or SV39gene product, e.g., construction of a fusion molecule in which all or afragment of the Pan5, Pan6, Pan7, SV1, SV25 or SV39 gene product isfused (either directly or via a linker) with a fusion partner to enhanceOther suitable modifications include, without limitation, truncation ofa coding region (e.g., a protein or enzyme) to eliminate a pre- orpro-protein ordinarily cleaved and to provide the mature protein orenzyme and/or mutation of a coding region to provide a secretable geneproduct. Still other modifications will be readily apparent to one ofskill in the art. The invention further encompasses proteins having atleast about 95% to 99% identity to the Pan5, Pan6, Pan7, SV1, SV25 orSV39 proteins provided herein.

As described herein, vectors of the invention containing the adenoviralcapsid proteins of the invention are particularly well suited for use inapplications in which the neutralizing antibodies diminish theeffectiveness of other Ad serotype based vectors, as well as other viralvectors. The rAd vectors of the invention are particularly advantageousin readministration for repeat gene therapy or for boosting immuneresponse (vaccine titers).

Under certain circumstances, it may be desirable to use one or more ofthe Pan5, Pan6, Pan7, SV1, SV25 and/or SV39 gene products (e.g., acapsid protein or a fragment thereof) to generate an antibody. The term“an antibody,” as used herein, refers to an immunoglobulin moleculewhich is able to specifically bind to an epitope. Thus, the antibodiesof the invention bind, preferably specifically and withoutcross-reactivity, to a Pan5, Pan6, Pan7, SV1, SV25 or SV39 epitope. Theantibodies in the present invention exist in a variety of formsincluding, for example, high affinity polyclonal antibodies, monoclonalantibodies, synthetic antibodies, chimeric antibodies, recombinantantibodies and humanized antibodies. Such antibodies originate fromimmunoglobulin classes IgG, IgM, IgA, IgD and IgE.

Such antibodies may be generated using any of a number of methods knowin the art. Suitable antibodies may be generated by well-knownconventional techniques, e.g. Kohler and Milstein and the many knownmodifications thereof. Similarly desirable high titer antibodies aregenerated by applying known recombinant techniques to the monoclonal orpolyclonal antibodies developed to these antigens [see, e.g., PCT PatentApplication No. PCT/GB85/00392; British Patent Application PublicationNo. GB2188638A; Amit et al., 1986 Science, 233:747-753; Queen et al.,1989 Proc. Nat'l. Acad. Sci. USA, 86:10029-10033; PCT Patent ApplicationNo. PCT/WO9007861; and Riechmann et al., Nature, 332:323-327 (1988);Huse et al, 1988a Science, 246:1275-1281]. Alternatively, antibodies canbe produced by manipulating the complementarity determining regions ofanimal or human antibodies to the antigen of this invention. See, e.g.,E. Mark and Padlin, “Humanization of Monoclonal Antibodies”, Chapter 4,The Handbook of Experimental Pharmacology, Vol. 113, The Pharmacology ofMonoclonal Antibodies, Springer-Verlag (June, 1994); Harlow et al.,1999, Using Antibodies: A Laboratory Manual, Cold Spring HarborLaboratory Press, NY; Harlow et al., 1989, Antibodies: A LaboratoryManual, Cold Spring Harbor, New York; Houston et al., 1988, Proc. Natl.Acad. Sci. USA 85:5879-5883; and Bird et al., 1988, Science 242:423-426.Further provided by the present invention are anti-idiotype antibodies(Ab2) and anti-anti-idiotype antibodies (Ab3). See, e.g., M. Wettendorffet al., “Modulation of anti-tumor immunity by anti-idiotypicantibodies.” In Idiotypic Network and Diseases, ed. by J. Cerny and J.Hiernaux, 1990 J. Am. Soc. Microbiol., Washington D.C.: pp. 203-229].These anti-idiotype and anti-anti-idiotype antibodies are produced usingtechniques well known to those of skill in the art. These antibodies maybe used for a variety of purposes, including diagnostic and clinicalmethods and kits.

Under certain circumstances, it may be desirable to introduce adetectable label or a tag onto a Pan5, Pan6, Pan7, SV1, SV25 or SV39gene product, antibody or other construct of the invention. As usedherein, a detectable label is a molecule which is capable, alone or uponinteraction with another molecule, of providing a detectable signal.Most desirably, the label is detectable visually, e.g. by fluorescence,for ready use in immunohistochemical analyses or immunofluorescentmicroscopy. For example, suitable labels include fluoresceinisothiocyanate (FITC), phycoerythrin (PE), allophycocyanin (APC),coriphosphine-O (CPO) or tandem dyes, PE-cyanin-5 (PC5), and PE-TexasRed (ECD). All of these fluorescent dyes are commercially available, andtheir uses known to the art. Other useful labels include a colloidalgold label. Still other useful labels include radioactive compounds orelements. Additionally, labels include a variety of enzyme systems thatoperate to reveal a colorimetric signal in an assay, e.g., glucoseoxidase (which uses glucose as a substrate) releases peroxide as aproduct which in the presence of peroxidase and a hydrogen donor such astetramethyl benzidine (TMB) produces an oxidized TMB that is seen as ablue color. Other examples include horseradish peroxidase (HRP) oralkaline phosphatase (AP), and hexokinase in conjunction withglucose-6-phosphate dehydrogenase which reacts with ATP, glucose, andNAD+ to yield, among other products, NADH that is detected as increasedabsorbance at 340 nm wavelength.

Other label systems that are utilized in the methods of this inventionare detectable by other means, e.g., colored latex microparticles [BangsLaboratories, Indiana] in which a dye is embedded are used in place ofenzymes to form conjugates with the target sequences provide a visualsignal indicative of the presence of the resulting complex in applicableassays.

Methods for coupling or associating the label with a desired moleculeare similarly conventional and known to those of skill in the art. Knownmethods of label attachment are described [see, for example, Handbook ofFluorescent probes and Research Chemicals, 6th Ed., R. P. M. Haugland,Molecular Probes, Inc., Eugene, Oreg., 1996; Pierce Catalog andHandbook, Life Science and Analytical Research Products, Pierce ChemicalCompany, Rockford, Ill., 1994/1995]. Thus, selection of the label andcoupling methods do not limit this invention.

The sequences, proteins, and fragments of the invention may be producedby any suitable means, including recombinant production, chemicalsynthesis, or other synthetic means. Suitable production techniques arewell known to those of skill in the art. See, e.g., Sambrook et al,Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Press (ColdSpring Harbor, N.Y.). Alternatively, peptides can also be synthesized bythe well known solid phase peptide synthesis methods (Merrifield, J. Am.Chem. Soc., 85:2149 (1962); Stewart and Young, Solid Phase PeptideSynthesis (Freeman, San Francisco, 1969) pp. 27-62). These and othersuitable production methods are within the knowledge of those of skillin the art and are not a limitation of the present invention.

In addition, one of skill in the art will readily understand that the Adsequences of the invention can be readily adapted for use for a varietyof viral and non-viral vector systems for in vitro, ex vivo or in vivodelivery of therapeutic and immunogenic molecules. For example, in oneembodiment, the simian Ad capsid proteins and other simian adenovirusproteins described herein are used for non-viral, protein-based deliveryof genes, proteins, and other desirable diagnostic, therapeutic andimmunogenic molecules. In one such embodiment, a protein of theinvention is linked, directly or indirectly, to a molecule for targetingto cells with a receptor for adenoviruses. Preferably, a capsid proteinsuch as a hexon, penton, fiber or a fragment thereof having a ligand fora cell surface receptor is selected for such targeting. Suitablemolecules for delivery are selected from among the therapeutic moleculesdescribed herein and their gene products. A variety of linkersincluding, lipids, polyLys, and the like may be utilized as linkers. Forexample, the simian penton protein may be readily utilized for such apurpose by production of a fusion protein using the simian pentonsequences in a manner analogous to that described in Medina-Kauwe L K,et al, Gene Ther. 2001 May; 8(10):795-803 and Medina-Kauwe L K, et al,Gene Ther. 2001 December; 8(23): 1753-1761. Alternatively, the aminoacid sequences of simian Ad protein IX may be utilized for targetingvectors to a cell surface receptor, as described in US Patent Appln20010047081. Suitable ligands include a CD40 antigen, an RGD-containingor polylysine-containing sequence, and the like. Still other simian Adproteins, including, e.g., the hexon protein and/or the fiber protein,may be used for used for these and similar purposes.

Still other adenoviral proteins of the invention may be used as alone,or in combination with other adenoviral protein, for a variety ofpurposes which will be readily apparent to one of skill in the art. Inaddition, still other uses for the adenoviral proteins of the inventionwill be readily apparent to one of skill in the art.

II. Recombinant Adenoviral Vectors

The compositions of this invention include vectors that deliver aheterologous molecule to cells, either for therapeutic or vaccinepurposes. As used herein, a vector may include any genetic elementincluding, without limitation, naked DNA, a phage, transposon, cosmid,episome, plasmid, or a virus. Such vectors contain simian adenovirus DNAof Pan5, Pan6, Pan7, SV1, SV25 and/or SV39 and a minigene. By “minigene”is meant the combination of a selected heterologous gene and the otherregulatory elements necessary to drive translation, transcription and/orexpression of the gene product in a host cell.

Typically, an adenoviral vector of the invention is designed such thatthe minigene is located in a nucleic acid molecule which contains otheradenoviral sequences in the region native to a selected adenoviral gene.The minigene may be inserted into an existing gene region to disrupt thefunction of that region, if desired. Alternatively, the minigene may beinserted into the site of a partially or fully deleted adenoviral gene.For example, the minigene may be located in the site of such as the siteof a functional E1 deletion or functional E3 deletion, among others thatmay be selected. The term “functionally deleted” or “functionaldeletion” means that a sufficient amount of the gene region is removedor otherwise damaged, e.g., by mutation or modification, so that thegene region is no longer capable of producing functional products ofgene expression. If desired, the entire gene region may be removed.Other suitable sites for gene disruption or deletion are discussedelsewhere in the application.

For example, for a production vector useful for generation of arecombinant virus, the vector may contain the minigene and either the 5′end of the adenoviral genome or the 3′ end of the adenoviral genome, orboth the 5′ and 3′ ends of the adenoviral genome. The 5′ end of theadenoviral genome contains the 5′ cis-elements necessary for packagingand replication; i.e., the 5′ inverted terminal repeat (ITR) sequences(which functions as origins of replication) and the native 5′ packagingenhancer domains (that contain sequences necessary for packaging linearAd genomes and enhancer elements for the E1 promoter). The 3′ end of theadenoviral genome includes the 3′ cis-elements (including the ITRs)necessary for packaging and encapsidation. Suitably, a recombinantadenovirus contains both 5′ and 3′ adenoviral cis-elements and theminigene is located between the 5′ and 3′ adenoviral sequences. Anyadenoviral vector of the invention may also contain additionaladenoviral sequences.

Suitably, these adenoviral vectors of the invention contain one or moreadenoviral elements derived from an adenoviral genome of the invention.In one embodiment, the vectors contain adenoviral ITRs from Pan5, Pan6,Pan7, SV1, SV25 or SV39 and additional adenoviral sequences from thesame adenoviral serotype. In another embodiment, the vectors containadenoviral sequences that are derived from a different

adenoviral serotype than that which provides the ITRs. As definedherein, a pseudotyped adenovirus refers to an adenovirus in which thecapsid protein of the adenovirus is from a different serotype than theserotype which provides the ITRs. The selection of the serotype of theITRs and the serotype of any other adenoviral sequences present invector is not a limitation of the present invention. A variety ofadenovirus strains are available from the American Type CultureCollection, Manassas, Va., or available by request from a variety ofcommercial and institutional sources. Further, the sequences of manysuch strains are available from a variety of databases including, e.g.,PubMed and GenBank. Homologous adenovirus vectors prepared from othersimian or from human adenoviruses are described in the publishedliterature [see, for example, U.S. Pat. No. 5,240,846]. The DNAsequences of a number of adenovirus types are available from GenBank,including type Ad5 [GenBank Accession No. M73260]. The adenovirussequences may be obtained from any known adenovirus serotype, such asserotypes 2, 3, 4, 7, 12 and 40, and further including any of thepresently identified human types. Similarly adenoviruses known to infectnon-human animals (e.g., simians) may also be employed in the vectorconstructs of this invention. See, e.g., U.S. Pat. No. 6,083,716.

The viral sequences, helper viruses, if needed, and recombinant viralparticles, and other vector components and sequences employed in theconstruction of the vectors described herein are obtained as describedabove. The DNA sequences of the Pan5, Pan6, Pan7, SV1, SV25 and/or SV39simian adenovirus sequences of the invention are employed to constructvectors and cell lines useful in the preparation of such vectors.

Modifications of the nucleic acid sequences forming the vectors of thisinvention, including sequence deletions, insertions, and other mutationsmay be generated using standard molecular biological techniques and arewithin the scope of this invention.

A. The “Minigene”

The methods employed for the selection of the transgene, the cloning andconstruction of the “minigene” and its insertion into the viral vectorare within the skill in the art given the teachings provided herein.

1. The Transgene

The transgene is a nucleic acid sequence, heterologous to the vectorsequences flanking the transgene, which encodes a polypeptide, protein,or other product, of interest. The nucleic acid coding sequence isoperatively linked to regulatory components in a manner which permitstransgene transcription, translation, and/or expression in a host cell.

The composition of the transgene sequence will depend upon the use towhich the resulting vector will be put. For example, one type oftransgene sequence includes a reporter sequence, which upon expressionproduces a detectable signal. Such reporter sequences include, withoutlimitation, DNA sequences encoding β-lactamase, β-galactosidase (LacZ),alkaline phosphatase, thymidine kinase, green fluorescent protein (GFP),chloramphenicol acetyltransferase (CAT), luciferase, membrane boundproteins including, for example, CD2, CD4, CD8, the influenzahemagglutinin protein, and others well known in the art, to which highaffinity antibodies directed thereto exist or can be produced byconventional means, and fusion proteins comprising a membrane boundprotein appropriately fused to an antigen tag domain from, among others,hemagglutinin or Myc. These coding sequences, when associated withregulatory elements which drive their expression, provide signalsdetectable by conventional means, including enzymatic, radiographic,colorimetric, fluorescence or other spectrographic assays, fluorescentactivating cell sorting assays and immunological assays, includingenzyme linked immunosorbent assay (ELISA), radioimmunoassay (RIA) andimmunohistochemistry. For example, where the marker sequence is the LacZgene, the presence of the vector carrying the signal is detected byassays for beta-galactosidase activity. Where the transgene is GFP orluciferase, the vector carrying the signal may be measured visually bycolor or light production in a luminometer.

However, desirably, the transgene is a non-marker sequence encoding aproduct which is useful in biology and medicine, such as proteins,peptides, RNA, enzymes, or catalytic RNAs. Desirable RNA moleculesinclude tRNA, dsRNA, ribosomal RNA, catalytic RNAs, and antisense RNAs.One example of a useful RNA sequence is a sequence which extinguishesexpression of a targeted nucleic acid sequence in the treated animal.

The transgene may be used for treatment, e.g., of genetic deficiencies,as a cancer therapeutic or vaccine, for induction of an immune response,and/or for prophylactic vaccine purposes. As used herein, induction ofan immune response refers to the ability of a molecule (e.g., a geneproduct) to induce a T cell and/or a humoral immune response to themolecule. The invention further includes using multiple transgenes,e.g., to correct or ameliorate a condition caused by a multi-subunitprotein. In certain situations, a different transgene may be used toencode each subunit of a protein, or to encode different peptides orproteins. This is desirable when the size of the DNA encoding theprotein subunit is large, e.g., for an immunoglobulin, theplatelet-derived growth factor, or a dystrophin protein. In order forthe cell to produce the multi-subunit protein, a cell is infected withthe recombinant virus containing each of the different subunits.Alternatively, different subunits of a protein may be encoded by thesame transgene. In this case, a single transgene includes the DNAencoding each of the subunits, with the DNA for each subunit separatedby an internal ribozyme entry site (IRES). This is desirable when thesize of the DNA encoding each of the subunits is small, e.g., the totalsize of the DNA encoding the subunits and the IRES is less than fivekilobases. As an alternative to an IRES, the DNA may be separated bysequences encoding a 2A peptide, which self-cleaves in apost-translational event. See, e.g., M. L. Donnelly, et al, J. Gen.Virol., 78(Pt 1):13-21 (January 1997); Furler, S., et al, Gene Ther.,8(11):864-873 (June 2001); Klump H., et al., Gene Ther., 8(10):811-817(May 2001). This 2A peptide is significantly smaller than an IRES,making it well suited for use when space is a limiting factor. However,the selected transgene may encode any biologically active product orother product, e.g., a product desirable for study.

Suitable transgenes may be readily selected by one of skill in the art.The selection of the transgene is not considered to be a limitation ofthis invention.

2. Regulatory Elements

In addition to the major elements identified above for the minigene, thevector also includes conventional control elements necessary which areoperably linked to the transgene in a manner that permits itstranscription, translation and/or expression in a cell transfected withthe plasmid vector or infected with the virus produced by the invention.As used herein, “operably linked” sequences include both expressioncontrol sequences that are contiguous with the gene of interest andexpression control sequences that act in trans or at a distance tocontrol the gene of interest.

Expression control sequences include appropriate transcriptioninitiation, termination, promoter and enhancer sequences; efficient RNAprocessing signals such as splicing and polyadenylation (polyA) signals;sequences that stabilize cytoplasmic mRNA; sequences that enhancetranslation efficiency (i.e., Kozak consensus sequence); sequences thatenhance protein stability; and when desired, sequences that enhancesecretion of the encoded product. A great number of expression controlsequences, including promoters which are native, constitutive, inducibleand/or tissue-specific, are known in the art and may be utilized.

Examples of constitutive promoters include, without limitation, theretroviral Rous sarcoma virus (RSV) LTR promoter (optionally with theRSV enhancer), the cytomegalovirus (CMV) promoter (optionally with theCMV enhancer) [see, e.g., Boshart et al, Cell, 41:521-530 (1985)], theSV40 promoter, the dihydrofolate reductase promoter, the β-actinpromoter, the phosphoglycerol kinase (PGK) promoter, and the EF1αpromoter [Invitrogen].

Inducible promoters allow regulation of gene expression and can beregulated by exogenously supplied compounds, environmental factors suchas temperature, or the presence of a specific physiological state, e.g.,acute phase, a particular differentiation state of the cell, or inreplicating cells only. Inducible promoters and inducible systems areavailable from a variety of commercial sources, including, withoutlimitation, Invitrogen, Clontech and Ariad. Many other systems have beendescribed and can be readily selected by one of skill in the art. Forexample, inducible promoters include the zinc-inducible sheepmetallothionine (MT) promoter and the dexamethasone (Dex)-induciblemouse mammary tumor virus (MMTV) promoter. Other inducible systemsinclude the T7 polymerase promoter system [WO 98/10088]; the ecdysoneinsect promoter [No et al, Proc. Natl. Acad. Sci. USA, 93:3346-3351(1996)], the tetracycline-repressible system [Gossen et al, Proc. Natl.Acad. Sci. USA, 89:5547-5551 (1992)], the tetracycline-inducible system[Gossen et al, Science, 268:1766-1769 (1995), see also Harvey et al,Curr. Opin. Chem. Biol., 2:512-518 (1998)]. Other systems include theFK506 dimer, VP16 or p65 using castradiol, diphenol murislerone, theRU486-inducible system [Wang et al, Nat. Biotech., 15:239-243 (1997) andWang et al, Gene Ther., 4:432-441 (1997)] and the rapamycin-induciblesystem [Magari et al, J. Clin. Invest., 100:2865-2872 (1997)]. Theeffectiveness of some inducible promoters increases over time. In suchcases one can enhance the effectiveness of such systems by insertingmultiple repressors in tandem, e.g., TetR linked to a TetR by an IRES.Alternatively, one can wait at least 3 days before screening for thedesired function. One can enhance expression of desired proteins byknown means to enhance the effectiveness of this system. For example,using the Woodchuck Hepatitis Virus Posttranscriptional RegulatoryElement (WPRE).

In another embodiment, the native promoter for the transgene will beused. The native promoter may be preferred when it is desired thatexpression of the transgene should mimic the native expression. Thenative promoter may be used when expression of the transgene must beregulated temporally or developmentally, or in a tissue-specific manner,or in response to specific transcriptional stimuli. In a furtherembodiment, other native expression control elements, such as enhancerelements, polyadenylation sites or Kozak consensus sequences may also beused to mimic the native expression.

Another embodiment of the transgene includes a transgene operably linkedto a tissue-specific promoter. For instance, if expression in skeletalmuscle is desired, a promoter active in muscle should be used. Theseinclude the promoters from genes encoding skeletal ∃-actin, myosin lightchain 2A, dystrophin, muscle creatine kinase, as well as syntheticmuscle promoters with activities higher than naturally occurringpromoters (see Li et al., Nat. Biotech., 17:241-245 (1999)). Examples ofpromoters that are tissue-specific are known for liver (albumin,Miyatake et al., J. Virol., 71:5124-32 (1997); hepatitis B virus corepromoter, Sandig et al., Gene Ther., 3:1002-9 (1996); alpha-fetoprotein(AFP), Arbuthnot et al., Hum. Gene Ther., 7:1503-14 (1996)), boneosteocalcin (Stein et al., Mol. Biol. Rep., 24:185-96 (1997)); bonesialoprotein (Chen et al., J. Bone Miner. Res., 11:654-64 (1996)),lymphocytes (CD2, Hansal et al., J. Immunol., 161:1063-8 (1998);immunoglobulin heavy chain; T cell receptor chain), neuronal such asneuron-specific enolase (NSE) promoter (Andersen et al., Cell. Mol.Neurobiol., 13:503-15 (1993)), neurofilament light-chain gene (Piccioliet al., Proc. Natl. Acad. Sci. USA, 88:5611-5 (1991)), and theneuron-specific vgf gene (Piccioli et al., Neuron, 15:373-84 (1995)),among others.

Optionally, vectors carrying transgenes encoding therapeutically usefulor immunogenic products may also include selectable markers or reportergenes may include sequences encoding geneticin, hygromicin or purimycinresistance, among others. Such selectable reporters or marker genes(preferably located outside the viral genome to be packaged into a viralparticle) can be used to signal the presence of the plasmids inbacterial cells, such as ampicillin resistance. Other components of thevector may include an origin of replication. Selection of these andother promoters and vector elements are conventional and many suchsequences are available [see, e.g., Sambrook et al, and references citedtherein].

These vectors are generated using the techniques and sequences providedherein, in conjunction with techniques known to those of skill in theart. Such techniques include conventional cloning techniques of cDNAsuch as those described in texts [Sambrook et al, Molecular Cloning: ALaboratory Manual, Cold Spring Harbor Press, Cold Spring Harbor, N.Y.],use of overlapping oligonucleotide sequences of the adenovirus genomes,polymerase chain reaction, and any suitable method which provides thedesired nucleotide sequence.

III. Production of the Recombinant Viral Particle

In one embodiment, the simian adenoviral plasmids (or other vectors) areused to produce recombinant adenoviral particles. In one embodiment, therecombinant adenoviruses are functionally deleted in the E1a or E1bgenes, and optionally bearing other mutations, e.g.,temperature-sensitive mutations or deletions in other genes. In otherembodiments, it is desirable to retain an intact E1a and/or E1b regionin the recombinant adenoviruses. Such an intact E1 region may be locatedin its native location in the adenoviral genome or placed in the site ofa deletion in the native adenoviral genome (e.g., in the E3 region).

In the construction of useful simian adenovirus vectors for delivery ofa gene to the human (or other mammalian) cell, a range of adenovirusnucleic acid sequences can be employed in the vectors. For example, allor a portion of the adenovirus delayed early gene E3 may be eliminatedfrom the simian adenovirus sequence which forms a part of therecombinant virus. The function of simian E3 is believed to beirrelevant to the function and production of the recombinant virusparticle. Simian adenovirus vectors may also be constructed having adeletion of at least the ORF6 region of the E4 gene, and more desirablybecause of the redundancy in the function of this region, the entire E4region. Still another vector of this invention contains a deletion inthe delayed early gene E2a. Deletions may also be made in any of thelate genes L1 through L5 of the simian adenovirus genome. Similarly,deletions in the intermediate genes IX and IVa₂ may be useful for somepurposes. Other deletions may be made in the other structural ornon-structural adenovirus genes. The above discussed deletions may beused individually, i.e., an adenovirus sequence for use in the presentinvention may contain deletions in only a single region. Alternatively,deletions of entire genes or portions thereof effective to destroy theirbiological activity may be used in any combination. For example, in oneexemplary vector, the adenovirus sequence may have deletions of the E1genes and the E4 gene, or of the E1, E2a and E3 genes, or of the E1 andE3 genes, or of E1, E2a and E4 genes, with or without deletion of E3,and so on. As discussed above, such deletions may be used in combinationwith other mutations, such as temperature-sensitive mutations, toachieve a desired result.

An adenoviral vector lacking any essential adenoviral sequences (e.g.,E1a, E1b, E2a, E2b, E4 ORF6, L1, L2, L3, L4 and L5) may be cultured inthe presence of the missing adenoviral gene products which are requiredfor viral infectivity and propagation of an adenoviral particle. Thesehelper functions may be provided by culturing the adenoviral vector inthe presence of one or more helper constructs (e.g., a plasmid or virus)or a packaging host cell. See, for example, the techniques described forpreparation of a “minimal” human Ad vector in International PatentApplication WO96/13597, published May 9, 1996, and incorporated hereinby reference.

1. Helper Viruses

Thus, depending upon the simian adenovirus gene content of the viralvectors employed to carry the minigene, a helper adenovirus ornon-replicating virus fragment may be necessary to provide sufficientsimian adenovirus gene sequences necessary to produce an infectiverecombinant viral particle containing the minigene. Useful helperviruses contain selected adenovirus gene sequences not present in theadenovirus vector construct and/or not expressed by the packaging cellline in which the vector is transfected. In one embodiment, the helpervirus is replication-defective and contains a variety of adenovirusgenes in addition to the sequences described above. Such a helper virusis desirably used in combination with an E1-expressing cell line.

Helper viruses may also be formed into poly-cation conjugates asdescribed in Wu et al, J. Biol. Chem., 264:16985-16987 (1989); K. J.Fisher and J. M. Wilson, Biochem. J., 299:49 (Apr. 1, 1994). Helpervirus may optionally contain a second reporter minigene. A number ofsuch reporter genes are known to the art. The presence of a reportergene on the helper virus which is different from the transgene on theadenovirus vector allows both the Ad vector and the helper virus to beindependently monitored. This second reporter is used to enableseparation between the resulting recombinant virus and the helper virusupon purification.

2. Complementation Cell Lines

To generate recombinant simian adenoviruses (Ad) deleted in any of thegenes described above, the function of the deleted gene region, ifessential to the replication and infectivity of the virus, must besupplied to the recombinant virus by a helper virus or cell line, i.e.,a complementation or packaging cell line. In many circumstances, a cellline expressing the human E1 can be used to transcomplement the chimp Advector. This is particularly advantageous because, due to the diversitybetween the chimp Ad sequences of the invention and the human AdE1sequences found in currently available packaging cells, the use of thecurrent human E1-containing cells prevents the generation ofreplication-competent adenoviruses during the replication and productionprocess. However, in certain circumstances, it will be desirable toutilize a cell line which expresses the E1 gene products can be utilizedfor production of an E1-deleted simian adenovirus. Such cell lines havebeen described. See, e.g., U.S. Pat. No. 6,083,716.

If desired, one may utilize the sequences provided herein to generate apackaging cell or cell line that expresses, at a minimum, the adenovirusE1 gene from Pan5, Pan6, Pan7, SV1, SV25 or SV39 under thetranscriptional control of a promoter for expression in a selectedparent cell line. Inducible or constitutive promoters may be employedfor this purpose. Examples of such promoters are described in detailelsewhere in this specification. A parent cell is selected for thegeneration of a novel cell line expressing any desired AdPan5, Pan6,Pan7, SV1, SV25 or SV39 gene. Without limitation, such a parent cellline may be HeLa [ATCC Accession No. CCL 2], A549 [ATCC Accession No.CCL 185], HEK 293, KB [CCL 17], Detroit [e.g., Detroit 510, CCL 72] andWI-38 [CCL 75] cells, among others. These cell lines are all availablefrom the American Type Culture Collection, 10801 University Boulevard,Manassas, Va. 20110-2209. Other suitable parent cell lines may beobtained from other sources.

Such E1-expressing cell lines are useful in the generation ofrecombinant simian adenovirus E1 deleted vectors. Additionally, oralternatively, the invention provides cell lines that express one ormore simian adenoviral gene products, e.g., E1a, E1b, E2a, and/or E4ORF6, can be constructed using essentially the same procedures for usein the generation of recombinant simian viral vectors. Such cell linescan be utilized to transcomplement adenovirus vectors deleted in theessential genes that encode those products, or to provide helperfunctions necessary for packaging of a helper-dependent virus (e.g.,adeno-associated virus). The preparation of a host cell according tothis invention involves techniques such as assembly of selected DNAsequences. This assembly may be accomplished utilizing conventionaltechniques. Such techniques include cDNA and genomic cloning, which arewell known and are described in Sambrook et al., cited above, use ofoverlapping oligonucleotide sequences of the adenovirus genomes,combined with polymerase chain reaction, synthetic methods, and anyother suitable methods which provide the desired nucleotide sequence.

In still another alternative, the essential adenoviral gene products areprovided in trans by the adenoviral vector and/or helper virus. In suchan instance, a suitable host cell can be selected from any biologicalorganism, including prokaryotic (e.g., bacterial) cells, and eukaryoticcells, including, insect cells, yeast cells and mammalian cells.Particularly desirable host cells are selected from among any mammalianspecies, including, without limitation, cells such as A549, WEHI, 3T3,10T1/2, HEK 293 cells or PERC6 (both of which express functionaladenoviral E1) [Fallaux, F J et al, (1998), Hum Gene Ther, 9:1909-1917],Saos, C2C12, L cells, HT1080, HepG2 and primary fibroblast, hepatocyteand myoblast cells derived from mammals including human, monkey, mouse,rat, rabbit, and hamster. The selection of the mammalian speciesproviding the cells is not a limitation of this invention; nor is thetype of mammalian cell, i.e., fibroblast, hepatocyte, tumor cell, etc.

3. Assembly of Viral Particle and Transfection of a Cell Line

Generally, when delivering the vector comprising the minigene bytransfection, the vector is delivered in an amount from about 5 μg toabout 100 μg DNA, and preferably about 10 to about 50 μg DNA to about1×10⁴ cells to about 1×10¹³ cells, and preferably about 10⁵ cells.However, the relative amounts of vector DNA to host cells may beadjusted, taking into consideration such factors as the selected vector,the delivery method and the host cells selected.

The vector may be any vector known in the art or disclosed above,including naked DNA, a plasmid, phage, transposon, cosmids, episomes,viruses, etc. Introduction into the host cell of the vector may beachieved by any means known in the art or as disclosed above, includingtransfection, and infection. One or more of the adenoviral genes may bestably integrated into the genome of the host cell, stably expressed asepisomes, or expressed transiently. The gene products may all beexpressed transiently, on an episome or stably integrated, or some ofthe gene products may be expressed stably while others are expressedtransiently. Furthermore, the promoters for each of the adenoviral genesmay be selected independently from a constitutive promoter, an induciblepromoter or a native adenoviral promoter. The promoters may be regulatedby a specific physiological state of the organism or cell (i.e., by thedifferentiation state or in replicating or quiescent cells) or byexogenously-added factors, for example.

Introduction of the molecules (as plasmids or viruses) into the hostcell may also be accomplished using techniques known to the skilledartisan and as discussed throughout the specification. In preferredembodiment, standard transfection techniques are used, e.g., CaPO₄transfection or electroporation.

Assembly of the selected DNA sequences of the adenovirus (as well as thetransgene and other vector elements into various intermediate plasmids,and the use of the plasmids and vectors to produce a recombinant viralparticle are all achieved using conventional techniques. Such techniquesinclude conventional cloning techniques of cDNA such as those describedin texts [Sambrook et al, cited above], use of overlappingoligonucleotide sequences of the adenovirus genomes, polymerase chainreaction, and any suitable method which provides the desired nucleotidesequence. Standard transfection and co-transfection techniques areemployed, e.g., CaPO₄ precipitation techniques. Other conventionalmethods employed include homologous recombination of the viral genomes,plaquing of viruses in agar overlay, methods of measuring signalgeneration, and the like.

For example, following the construction and assembly of the desiredminigene-containing viral vector, the vector is transfected in vitro inthe presence of a helper virus into the packaging cell line. Homologousrecombination occurs between the helper and the vector sequences, whichpermits the adenovirus-transgene sequences in the vector to bereplicated and packaged into virion capsids, resulting in therecombinant viral vector particles. The current method for producingsuch virus particles is transfection-based. However, the invention isnot limited to such methods.

The resulting recombinant simian adenoviruses are useful in transferringa selected transgene to a selected cell. In in vivo experiments with therecombinant virus grown in the packaging cell lines, the E1-deletedrecombinant simian adenoviral vectors of the invention demonstrateutility in transferring a transgene to a non-simian, preferably a human,cell.

IV. Use of the Recombinant Adenovirus Vectors

The recombinant simian adenovirus vectors of the invention are usefulfor gene transfer to a human or non-simian veterinary patient in vitro,ex vivo, and in vivo.

The recombinant adenovirus vectors described herein can be used asexpression vectors for the production of the products encoded by theheterologous genes in vitro. For example, the recombinant adenovirusescontaining a gene inserted into the location of an E1 deletion may betransfected into an E1-expressing cell line as described above.Alternatively, replication-competent adenoviruses may be used in anotherselected cell line. The transfected cells are then cultured in theconventional manner, allowing the recombinant adenovirus to express thegene product from the promoter. The gene product may then be recoveredfrom the culture medium by known conventional methods of proteinisolation and recovery from culture.

A Pan5, Pan6, Pan7, SV1, SV25 or SV39-derived recombinant simianadenoviral vector of the invention provides an efficient gene transfervehicle that can deliver a selected transgene to a selected host cell invivo or ex vivo even where the organism has neutralizing antibodies toone or more AAV serotypes. In one embodiment, the rAAV and the cells aremixed ex vivo; the infected cells are cultured using conventionalmethodologies; and the transduced cells are re-infused into the patient.These compositions are particularly well suited to gene delivery fortherapeutic purposes and for immunization, including inducing protectiveimmunity.

More commonly, the Pan 5, Pan6, Pan7, SV1, SV25, or SV39 recombinantadenoviral vectors of the invention will be utilized for delivery oftherapeutic or immunogenic molecules, as described below. It will bereadily understood for both applications, that the recombinantadenoviral vectors of the invention are particularly well suited for usein regimens involving repeat delivery of recombinant adenoviral vectors.Such regimens typically involve delivery of a series of viral vectors inwhich the viral capsids are alternated. The viral capsids may be changedfor each subsequent administration, or after a pre-selected number ofadministrations of a particular serotype capsid (e.g., one, two, three,four or more). Thus, a regimen may involve delivery of a rAd with afirst simian capsid, delivery with a rAd with a second simian capsid,and delivery with a third simian capsid. A variety of other regimenswhich use the Ad capsids of the invention alone, in combination with oneanother, or in combination with other Ad serotypes will be apparent tothose of skill in the art. Optionally, such a regimen may involveadministration of rAd with capsids of other non-human primateadenoviruses, human adenoviruses, or artificial serotypes such as aredescribed herein. Each phase of the regimen may involve administrationof a series of injections (or other delivery routes) with a single Adserotype capsid followed by a series with another Ad serotype capsid.Alternatively, the recombinant Ad vectors of the invention may beutilized in regimens involving other non-adenoviral-mediated deliverysystems, including other viral systems, non-viral delivery systems,protein, peptides, and other biologically active molecules.

The following sections will focus on exemplary molecules which may bedelivered via the adenoviral vectors of the invention.

A. Ad-Mediated Delivery of Therapeutic Molecules

In one embodiment, the above-described recombinant vectors areadministered to humans according to published methods for gene therapy.A simian viral vector bearing the selected transgene may be administeredto a patient, preferably suspended in a biologically compatible solutionor pharmaceutically acceptable delivery vehicle. A suitable vehicleincludes sterile saline. Other aqueous and non-aqueous isotonic sterileinjection solutions and aqueous and non-aqueous sterile suspensionsknown to be pharmaceutically acceptable carriers and well known to thoseof skill in the art may be employed for this purpose.

The simian adenoviral vectors are administered in sufficient amounts totransduce the target cells and to provide sufficient levels of genetransfer and expression to provide a therapeutic benefit without undueadverse or with medically acceptable physiological effects, which can bedetermined by those skilled in the medical arts. Conventional andpharmaceutically acceptable routes of administration include, but arenot limited to, direct delivery to the retina and other intraoculardelivery methods, direct delivery to the liver, inhalation, intranasal,intravenous, intramuscular, intratracheal, subcutaneous, intradermal,rectal, oral and other parenteral routes of administration. Routes ofadministration may be combined, if desired, or adjusted depending uponthe transgene or the condition. The route of administration primarilywill depend on the nature of the condition being treated.

Dosages of the viral vector will depend primarily on factors such as thecondition being treated, the age, weight and health of the patient, andmay thus vary among patients. For example, a therapeutically effectiveadult human or veterinary dosage of the viral vector is generally in therange of from about 100 μL to about 100 mL of a carrier containingconcentrations of from about 1×10⁶ to about 1×10¹⁵ particles, about1×10¹¹ to 1×10¹³ particles, or about 1×10⁹ to 1×10¹² particles virus.Dosages will range depending upon the size of the animal and the routeof administration. For example, a suitable human or veterinary dosage(for about an 80 kg animal) for intramuscular injection is in the rangeof about 1×10⁹ to about 5×10¹² particles per mL, for a single site.Optionally, multiple sites of administration may be delivered. Inanother example, a suitable human or veterinary dosage may be in therange of about 1×10¹¹ to about 1×10¹⁵ particles for an oral formulation.One of skill in the art may adjust these doses, depending the route ofadministration, and the therapeutic or vaccinal application for whichthe recombinant vector is employed. The levels of expression of thetransgene, or for an immunogen, the level of circulating antibody, canbe monitored to determine the frequency of dosage administration. Yetother methods for determining the timing of frequency of administrationwill be readily apparent to one of skill in the art.

An optional method step involves the co-administration to the patient,either concurrently with, or before or after administration of the viralvector, of a suitable amount of a short acting immune modulator. Theselected immune modulator is defined herein as an agent capable ofinhibiting the formation of neutralizing antibodies directed against therecombinant vector of this invention or capable of inhibiting cytolyticT lymphocyte (CTL) elimination of the vector. The immune modulator mayinterfere with the interactions between the T helper subsets (T_(H1) orT_(H2)) and B cells to inhibit neutralizing antibody formation.Alternatively, the immune modulator may inhibit the interaction betweenT_(H1) cells and CTLs to reduce the occurrence of CTL elimination of thevector. A variety of useful immune modulators and dosages for use ofsame are disclosed, for example, in Yang et al., J. Virol., 70(9)(September, 1996); International Patent Application No. WO96/12406,published May 2, 1996; and International Patent Application No.PCT/US96/03035, all incorporated herein by reference.

1. Therapeutic Transgenes

Useful therapeutic products encoded by the transgene include hormonesand growth and differentiation factors including, without limitation,insulin, glucagon, growth hormone (GH), parathyroid hormone (PTH),growth hormone releasing factor (GRF), follicle stimulating hormone(FSH), luteinizing hormone (LH), human chorionic gonadotropin (hCG),vascular endothelial growth factor (VEGF), angiopoietins, angiostatin,granulocyte colony stimulating factor (GCSF), erythropoietin (EPO),connective tissue growth factor (CTGF), basic fibroblast growth factor(bFGF), acidic fibroblast growth factor (aFGF), epidermal growth factor(EGF), transforming growth factor (TGF), platelet-derived growth factor(PDGF), insulin growth factors I and II (IGF-I and IGF-II), any one ofthe transforming growth factor superfamily, including TGF, activins,inhibins, or any of the bone morphogenic proteins (BMP) BMPs 1-15, anyone of the heregluin/neuregulin/ARIA/neu differentiation factor (NDF)family of growth factors, nerve growth factor (NGF), brain-derivedneurotrophic factor (BDNF), neurotrophins NT-3 and NT-4/5, ciliaryneurotrophic factor (CNTF), glial cell line derived neurotrophic factor(GDNF), neurturin, agrin, any one of the family ofsemaphorins/collapsins, netrin-1 and netrin-2, hepatocyte growth factor(HGF), ephrins, noggin, sonic hedgehog and tyrosine hydroxylase.

Other useful transgene products include proteins that regulate theimmune system including, without limitation, cytokines and lymphokinessuch as thrombopoietin (TPO), interleukins (IL) IL-1 through IL-25(including, e.g., IL-2, IL-4, IL-12 and IL-18), monocyte chemoattractantprotein, leukemia inhibitory factor, granulocyte-macrophage colonystimulating factor, Fas ligand, tumor necrosis factors and, interferons,and, stem cell factor, flk-2/flt3 ligand. Gene products produced by theimmune system are also useful in the invention. These include, withoutlimitation, immunoglobulins IgG, IgM, IgA, IgD and IgE, chimericimmunoglobulins, humanized antibodies, single chain antibodies, T cellreceptors, chimeric T cell receptors, single chain T cell receptors,class I and class II MHC molecules, as well as engineeredimmunoglobulins and MHC molecules. Useful gene products also includecomplement regulatory proteins such as complement regulatory proteins,membrane cofactor protein (MCP), decay accelerating factor (DAF), CR1,CF2 and CD59.

Still other useful gene products include any one of the receptors forthe hormones, growth factors, cytokines, lymphokines, regulatoryproteins and immune system proteins. The invention encompasses receptorsfor cholesterol regulation, including the low density lipoprotein (LDL)receptor, high density lipoprotein (HDL) receptor, the very low densitylipoprotein (VLDL) receptor, and the scavenger receptor. The inventionalso encompasses gene products such as members of the steroid hormonereceptor superfamily including glucocorticoid receptors and estrogenreceptors, Vitamin D receptors and other nuclear receptors. In addition,useful gene products include transcription factors such as jun, fos,max, mad, serum response factor (SRF), AP-1, AP2, myb, MyoD andmyogenin, ETS-box containing proteins, TFE3, E2F, ATF1, ATF2, ATF3,ATF4, ZF5, NFAT, CREB, HNF-4, C/EBP, SP1, CCAAT-box binding proteins,interferon regulation factor (IRF-1), Wilms tumor protein, ETS-bindingprotein, STAT, GATA-box binding proteins, e.g., GATA-3, and the forkheadfamily of winged helix proteins.

Other useful gene products include, carbamoyl synthetase I, ornithinetranscarbamylase, arginosuccinate synthetase, arginosuccinate lyase,arginase, fumarylacetacetate hydrolase, phenylalanine hydroxylase,alpha-1 antitrypsin, glucose-6-phosphatase, porphobilinogen deaminase,factor VIII, factor IX, cystathione beta-synthase, branched chainketoacid decarboxylase, albumin, isovaleryl-coA dehydrogenase, propionylCoA carboxylase, methyl malonyl CoA mutase, glutaryl CoA dehydrogenase,insulin, beta-glucosidase, pyruvate carboxylate, hepatic phosphorylase,phosphorylase kinase, glycine decarboxylase, H-protein, T-protein, acystic fibrosis transmembrane regulator (CFTR) sequence, and adystrophin cDNA sequence.

Other useful gene products include non-naturally occurring polypeptides,such as chimeric or hybrid polypeptides having a non-naturally occurringamino acid sequence containing insertions, deletions or amino acidsubstitutions. For example, single-chain engineered immunoglobulinscould be useful in certain immunocompromised patients. Other types ofnon-naturally occurring gene sequences include antisense molecules andcatalytic nucleic acids, such as ribozymes, which could be used toreduce overexpression of a target.

Reduction and/or modulation of expression of a gene are particularlydesirable for treatment of hyperproliferative conditions characterizedby hyperproliferating cells, as are cancers and psoriasis. Targetpolypeptides include those polypeptides which are produced exclusivelyor at higher levels in hyperproliferative cells as compared to normalcells. Target antigens include polypeptides encoded by oncogenes such asmyb, myc, fyn, and the translocation gene bcr/abl, ras, src, P53, neu,trk and EGRF. In addition to oncogene products as target antigens,target polypeptides for anti-cancer treatments and protective regimensinclude variable regions of antibodies made by B cell lymphomas andvariable regions of T cell receptors of T cell lymphomas which, in someembodiments, are also used as target antigens for autoimmune disease.Other tumor-associated polypeptides can be used as target polypeptidessuch as polypeptides which are found at higher levels in tumor cellsincluding the polypeptide recognized by monoclonal antibody 17-1A andfolate binding polypeptides.

Other suitable therapeutic polypeptides and proteins include those whichmay be useful for treating individuals suffering from autoimmunediseases and disorders by conferring a broad based protective immuneresponse against targets that are associated with autoimmunity includingcell receptors and cells which produce self-directed antibodies. T cellmediated autoimmune diseases include Rheumatoid arthritis (RA), multiplesclerosis (MS), Sjögren's syndrome, sarcoidosis, insulin dependentdiabetes mellitus (IDDM), autoimmune thyroiditis, reactive arthritis,ankylosing spondylitis, scleroderma, polymyositis, dermatomyositis,psoriasis, vasculitis, Wegener's granulomatosis, Crohn's disease andulcerative colitis. Each of these diseases is characterized by T cellreceptors (TCRs) that bind to endogenous antigens and initiate theinflammatory cascade associated with autoimmune diseases.

The simian adenoviral vectors of the invention are particularly wellsuited for therapeutic regimens in which multiple adenoviral-mediateddeliveries of transgenes is desired, e.g., in regimens involvingredelivery of the same transgene or in combination regimens involvingdelivery of other transgenes. Such regimens may involve administrationof a Pan5, Pan6, Pan7, SV1, SV25 or SV39 simian adenoviral vector,followed by re-administration with a vector from the same serotypeadenovirus. Particularly desirable regimens involve administration of aPan5, Pan6, Pan7, SV1, SV25 or SV39 simian adenoviral vector of theinvention, in which the serotype of the viral vector delivered in thefirst administration differs from the serotype of the viral vectorutilized in one or more of the subsequent administrations. For example,a therapeutic regimen involves administration of a Pan5, Pan6, Pan7,SV1, SV25 or SV39 vector and repeat administration with one or moreadenoviral vectors of the same or different serotypes. In anotherexample, a therapeutic regimen involves administration of an adenoviralvector followed by repeat administration with a Pan5, Pan6, Pan7, SV1,SV25 or SV39 vector of the invention which differs from the serotype ofthe first delivered adenoviral vector, and optionally furtheradministration with another vector which is the same or, preferably,differs from the serotype of the vector in the prior administrationsteps. These regimens are not limited to delivery of adenoviral vectorsconstructed using the Pan5, Pan6, Pan7, SV1, SV25 or SV39 simianserotypes of the invention. Rather, these regimens can readily utilizevectors other adenoviral serotypes, including, without limitation, othersimian adenoviral serotypes (e.g., Pan9 or C68, C1, etc), othernon-human primate adenoviral serotypes, or human adenoviral serotypes,in combination with one or more of the Pan5, Pan6, Pan7, SV1, SV25 orSV39 vectors of the invention. Examples of such simian, other non-humanprimate and human adenoviral serotypes are discussed elsewhere in thisdocument. Further, these therapeutic regimens may involve eithersimultaneous or sequential delivery of Pan 5, Pan6, Pan7, SV1, SV25,and/or SV39 adenoviral vectors of the invention in combination withnon-adenoviral vectors, non-viral vectors, and/or a variety of othertherapeutically useful compounds or molecules. The present invention isnot limited to these therapeutic regimens, a variety of which will bereadily apparent to one of skill in the art.

B. Ad-Mediated Delivery of Immunogenic Transgenes

The recombinant simian adenoviruses may also be employed as immunogeniccompositions. As used herein, an immunogenic composition is acomposition to which a humoral (e.g., antibody) or cellular (e.g., acytotoxic T cell) response is mounted to a transgene product deliveredby the immunogenic composition following delivery to a mammal, andpreferably a primate. The present invention provides a recombinantsimian Ad that can contain in any of its adenovirus sequence deletions agene encoding a desired immunogen. The simian adenovirus is likely to bebetter suited for use as a live recombinant virus vaccine in differentanimal species compared to an adenovirus of human origin, but is notlimited to such a use. The recombinant adenoviruses can be used asprophylactic or therapeutic vaccines against any pathogen for which theantigen(s) crucial for induction of an immune response and able to limitthe spread of the pathogen has been identified and for which the cDNA isavailable.

Such vaccinal (or other immunogenic) compositions are formulated in asuitable delivery vehicle, as described above. Generally, doses for theimmunogenic compositions are in the range defined above for therapeuticcompositions. The levels of immunity of the selected gene can bemonitored to determine the need, if any, for boosters. Following anassessment of antibody titers in the serum, optional boosterimmunizations may be desired.

Optionally, a vaccinal composition of the invention may be formulated tocontain other components, including, e.g. adjuvants, stabilizers, pHadjusters, preservatives and the like. Such components are well known tothose of skill in the vaccine art. Examples of suitable adjuvantsinclude, without limitation, liposomes, alum, monophosphoryl lipid A,and any biologically active factor, such as cytokine, an interleukin, achemokine, a ligands, and optimally combinations thereof. Certain ofthese biologically active factors can be expressed in vivo, e.g., via aplasmid or viral vector. For example, such an adjuvant can beadministered with a priming DNA vaccine encoding an antigen to enhancethe antigen-specific immune response compared with the immune responsegenerated upon priming with a DNA vaccine encoding the antigen only.

The recombinant adenoviruses are administered in a “an immunogenicamount”, that is, an amount of recombinant adenovirus that is effectivein a route of administration to transfect the desired cells and providesufficient levels of expression of the selected gene to induce an immuneresponse. Where protective immunity is provided, the recombinantadenoviruses are considered to be vaccine compositions useful inpreventing infection and/or recurrent disease.

Alternatively, or in addition, the vectors of the invention may containa transgene encoding a peptide, polypeptide or protein which induces animmune response to a selected immunogen. The recombinant adenoviruses ofthis invention are expected to be highly efficacious at inducingcytolytic T cells and antibodies to the inserted heterologous antigenicprotein expressed by the vector.

For example, immunogens may be selected from a variety of viralfamilies. Example of desirable viral families against which an immuneresponse would be desirable include, the picornavirus family, whichincludes the genera rhinoviruses, which are responsible for about 50% ofcases of the common cold; the genera enteroviruses, which includepolioviruses, coxsackieviruses, echoviruses, and human enterovirusessuch as hepatitis A virus; and the genera apthoviruses, which areresponsible for foot and mouth diseases, primarily in non-human animals.Within the picornavirus family of viruses, target antigens include theVP1, VP2, VP3, VP4, and VPG. Another viral family includes thecalcivirus family, which encompasses the Norwalk group of viruses, whichare an important causative agent of epidemic gastroenteritis. Stillanother viral family desirable for use in targeting antigens forinducing immune responses in humans and non-human animals is thetogavirus family, which includes the genera alphavirus, which includeSindbis viruses, RossRiver virus, and Venezuelan, Eastern & WesternEquine encephalitis, and rubivirus, including Rubella virus. Theflaviviridae family includes dengue, yellow fever, Japaneseencephalitis, St. Louis encephalitis and tick borne encephalitisviruses. Other target antigens may be generated from the Hepatitis C orthe coronavirus family, which includes a number of non-human virusessuch as infectious bronchitis virus (poultry), porcine transmissiblegastroenteric virus (pig), porcine hemagglutinating encephalomyelitisvirus (pig), feline infectious peritonitis virus (cats), feline entericcoronavirus (cat), canine coronavirus (dog), and human respiratorycoronaviruses, which may cause the common cold and/or non-A, B or Chepatitis. Within the coronavirus family, target antigens include the E1(also called M or matrix protein), E2 (also called S or Spike protein),E3 (also called HE or hemagglutin-elterose) glycoprotein (not present inall coronaviruses), or N (nucleocapsid). Still other antigens may betargeted against the rhabdovirus family, which includes the generavesiculovirus (e.g., Vesicular Stomatitis Virus), and the generallyssavirus (e.g., rabies). Within the rhabdovirus family, suitableantigens may be derived from the G protein or the N protein. The familyfiloviridae, which includes hemorrhagic fever viruses such as Marburgand Ebola virus, may be a suitable source of antigens. The paramyxovirusfamily includes parainfluenza Virus Type 1, parainfluenza Virus Type 3,bovine parainfluenza Virus Type 3, rubulavirus (mumps virus),parainfluenza Virus Type 2, parainfluenza virus Type 4, Newcastledisease virus (chickens), rinderpest, morbillivirus, which includesmeasles and canine distemper, and pneumovirus, which includesrespiratory syncytial virus. The influenza virus is classified withinthe family orthomyxovirus and is a suitable source of antigen (e.g., theHA protein, the N1 protein). The bunyavirus family includes the generabunyavirus (California encephalitis, La Crosse), phlebovirus (RiftValley Fever), hantavirus (puremala is a hemahagin fever virus),nairovirus (Nairobi sheep disease) and various unassigned bungaviruses.The arenavirus family provides a source of antigens against LCM andLassa fever virus. The reovirus family includes the genera reovirus,rotavirus (which causes acute gastroenteritis in children), orbiviruses,and cultivirus (Colorado Tick fever, Lebombo (humans), equineencephalosis, blue tongue).

The retrovirus family includes the sub-family oncorivirinal whichencompasses such human and veterinary diseases as feline leukemia virus,HTLVI and HTLVII, lentivirinal (which includes human immunodeficiencyvirus (HIV), simian immunodeficiency virus (SIV), felineimmunodeficiency virus (FIV), equine infectious anemia virus, andspumavirinal). Among the lentiviruses, many suitable antigens have beendescribed and can readily be selected. Examples of suitable HIV and SIVantigens include, without limitation the gag, pol, Vif, Vpx, VPR, Env,Tat, Nef, and Rev proteins, as well as various fragments thereof. Forexample, suitable fragments of the Env protein may include any of itssubunits such as the gp120, gp160, gp41, or smaller fragments thereof,e.g., of at least about 8 amino acids in length. Similarly, fragments ofthe tat protein may be selected. [See, U.S. Pat. No. 5,891,994 and U.S.Pat. No. 6,193,981.] See, also, the HIV and SIV proteins described in D.H. Barouch et al, J. Virol., 75(5):2462-2467 (March 2001), and R. R.Amara, et al, Science, 292:69-74 (6 Apr. 2001). In another example, theHIV and/or SIV immunogenic proteins or peptides may be used to formfusion proteins or other immunogenic molecules. See, e.g., the HIV-1 Tatand/or Nef fusion proteins and immunization regimens described in WO01/54719, published Aug. 2, 2001, and WO 99/16884, published Apr. 8,1999. The invention is not limited to the HIV and/or SIV immunogenicproteins or peptides described herein. In addition, a variety ofmodifications to these proteins have been described or could readily bemade by one of skill in the art. See, e.g., the modified gag proteinthat is described in U.S. Pat. No. 5,972,596. Further, any desired HIVand/or SIV immunogens may be delivered alone or in combination. Suchcombinations may include expression from a single vector or frommultiple vectors. Optionally, another combination may involve deliveryof one or more expressed immunogens with delivery of one or more of theimmunogens in protein form. Such combinations are discussed in moredetail below.

The papovavirus family includes the sub-family polyomaviruses (BKU andJCU viruses) and the sub-family papillomavirus (associated with cancersor malignant progression of papilloma). The adenovirus family includesviruses (EX, AD7, ARD, O.B.) which cause respiratory disease and/orenteritis. The parvovirus family feline parvovirus (feline enteritis),feline panleucopeniavirus, canine parvovirus, and porcine parvovirus.The herpesvirus family includes the sub-family alphaherpesvirinae, whichencompasses the genera simplexvirus (HSVI, HSVII), varicellovirus(pseudorabies, varicella zoster) and the sub-family betaherpesvirinae,which includes the genera cytomegalovirus (HCMV, muromegalovirus) andthe sub-family gammaherpesvirinae, which includes the generalymphocryptovirus, EBV (Burkitts lymphoma), infectious rhinotracheitis,Marek's disease virus, and rhadinovirus. The poxvirus family includesthe sub-family chordopoxvirinae, which encompasses the generaorthopoxvirus (Variola (Smallpox) and Vaccinia (Cowpox)), parapoxvirus,avipoxvirus, capripoxvirus, leporipoxvirus, suipoxvirus, and thesub-family entomopoxvirinae. The hepadnavirus family includes theHepatitis B virus. One unclassified virus which may be suitable sourceof antigens is the Hepatitis delta virus. Still other viral sources mayinclude avian infectious bursal disease virus and porcine respiratoryand reproductive syndrome virus. The alphavirus family includes equinearteritis virus and various Encephalitis viruses.

The present invention may also encompass immunogens which are useful toimmunize a human or non-human animal against other pathogens includingbacteria, fungi, parasitic microorganisms or multicellular parasiteswhich infect human and non-human vertebrates, or from a cancer cell ortumor cell. Examples of bacterial pathogens include pathogenicgram-positive cocci include pneumococci; staphylococci; andstreptococci. Pathogenic gram-negative cocci include meningococcus;gonococcus. Pathogenic enteric gram-negative bacilli includeenterobacteriaceae; pseudomonas, acinetobacteria and eikenella;melioidosis; salmonella; shigella; haemophilus; moraxella; H. ducreyi(which causes chancroid); brucella; Franisella tularensis (which causestularemia); yersinia (pasteurella); streptobacillus moniliformis andspirillum; Gram-positive bacilli include listeria monocytogenes;erysipelothrix rhusiopathiae; Corynebacterium diphtheria (diphtheria);cholera; B. anthracia (anthrax); donovanosis (granuloma inguinale); andbartonellosis. Diseases caused by pathogenic anaerobic bacteria includetetanus; botulism; other clostridia; tuberculosis; leprosy; and othermycobacteria. Pathogenic spirochetal diseases include syphilis;treponematoses: yaws, pinta and endemic syphilis; and leptospirosis.Other infections caused by higher pathogen bacteria and pathogenic fungiinclude actinomycosis; nocardiosis; cryptococcosis, blastomycosis,histoplasmosis and coccidioidomycosis; candidiasis, aspergillosis, andmucormycosis; sporotrichosis; paracoccidiodomycosis, petriellidiosis,torulopsosis, mycetoma and chromomycosis; and dermatophytosis.Rickettsial infections include Typhus fever, Rocky Mountain spottedfever, Q fever, and Rickettsialpox. Examples of mycoplasma andchlamydial infections include: mycoplasma pneumoniae; lymphogranulomavenereum; psittacosis; and perinatal chlamydial infections. Pathogeniceukaryotes encompass pathogenic protozoans and helminths and infectionsproduced thereby include: amebiasis; malaria; leishmaniasis;trypanosomiasis; toxoplasmosis; Pneumocystis carinii; Trichans;Toxoplasma gondii; babesiosis; giardiasis; trichinosis; filariasis;schistosomiasis; nematodes; trematodes or flukes; and cestode (tapeworm)infections.

Many of these organisms and/or toxins produced thereby have beenidentified by the Centers for Disease Control [(CDC), Department ofHeath and Human Services, USA], as agents which have potential for usein biological attacks. For example, some of these biological agents,include, Bacillus anthracis (anthrax), Clostridium botulinum and itstoxin (botulism), Yersinia pestis (plague), variola major (smallpox),Francisella tularensis (tularemia), and viral hemorrhagic fevers[filoviruses (e.g., Ebola, Marburg], and arenaviruses [e.g., Lassa,Machupo]), all of which are currently classified as Category A agents;Coxiella burnetti (Q fever); Brucella species (brucellosis),Burkholderia mallei (glanders), Burkholderia pseudomallei (meloidosis),Ricinus communis and its toxin (ricin toxin), Clostridium perfringensand its toxin (epsilon toxin), Staphylococcus species and their toxins(enterotoxin B), Chlamydia psittaci (psittacosis), water safety threats(e.g., Vibrio cholerae, Crytosporidium parvum), Typhus fever (Richettsiapowazekii), and viral encephalitis (alphaviruses, e.g., Venezuelanequine encephalitis; eastern equine encephalitis; western equineencephalitis); all of which are currently classified as Category Bagents; and Nipan virus and hantaviruses, which are currently classifiedas Category C agents. In addition, other organisms, which are soclassified or differently classified, may be identified and/or used forsuch a purpose in the future. It will be readily understood that theviral vectors and other constructs described herein are useful todeliver antigens from these organisms, viruses, their toxins or otherby-products, which will prevent and/or treat infection or other adversereactions with these biological agents.

Administration of the vectors of the invention to deliver immunogensagainst the variable region of the T cells elicit an immune responseincluding CTLs to eliminate those T cells. In RA, several specificvariable regions of TCRs which are involved in the disease have beencharacterized. These TCRs include V-3, V-14, V-17 and Vα-17. Thus,delivery of a nucleic acid sequence that encodes at least one of thesepolypeptides will elicit an immune response that will target T cellsinvolved in RA. In MS, several specific variable regions of TCRs whichare involved in the disease have been characterized. These TCRs includeV-7 and Vα-10. Thus, delivery of a nucleic acid sequence that encodes atleast one of these polypeptides will elicit an immune response that willtarget T cells involved in MS. In scleroderma, several specific variableregions of TCRs which are involved in the disease have beencharacterized. These TCRs include V-6, V-8, V-14 and Vα-16, Vα-3C, Vα-7,Vα-14, Vα-15, Vα-16, Vα-28 and Vα-12. Thus, delivery of a recombinantsimian adenovirus that encodes at least one of these polypeptides willelicit an immune response that will target T cells involved inscleroderma.

C. Ad-Mediated Delivery Methods

The therapeutic levels, or levels of immunity, of the selected gene canbe monitored to determine the need, if any, for boosters. Following anassessment of CD8+ T cell response, or optionally, antibody titers, inthe serum, optional booster immunizations may be desired. Optionally,the recombinant simian adenoviral vectors of the invention may bedelivered in a single administration or in various combination regimens,e.g., in combination with a regimen or course of treatment involvingother active ingredients or in a prime-boost regimen. A variety of suchregimens have been described in the art and may be readily selected.

For example, prime-boost regimens may involve the administration of aDNA (e.g., plasmid) based vector to prime the immune system to second,booster, administration with a traditional antigen, such as a protein ora recombinant virus carrying the sequences encoding such an antigen.See, e.g., WO 00/11140, published Mar. 2, 2000, incorporated byreference. Alternatively, an immunization regimen may involve theadministration of a recombinant simian adenoviral vector of theinvention to boost the immune response to a vector (either viral orDNA-based) carrying an antigen, or a protein. In still anotheralternative, an immunization regimen involves administration of aprotein followed by booster with a vector encoding the antigen.

In one embodiment, the invention provides a method of priming andboosting an immune response to a selected antigen by delivering aplasmid DNA vector carrying said antigen, followed by boosting with arecombinant simian adenoviral vector of the invention. In oneembodiment, the prime-boost regimen involves the expression ofmultiproteins from the prime and/or the boost vehicle. See, e.g., R. R.Amara, Science, 292:69-74 (6 Apr. 2001) which describes a multiproteinregimen for expression of protein subunits useful for generating animmune response against HIV and SIV. For example, a DNA prime maydeliver the Gag, Pol, Vif, VPX and Vpr and Env, Tat, and Rev from asingle transcript. Alternatively, the SIV Gag, Pol and HIV-1 Env isdelivered in a recombinant adenovirus construct of the invention. Stillother regimens are described in WO 99/16884 and WO 01/54719.

However, the prime-boost regimens are not limited to immunization forHIV or to delivery of these antigens. For example, priming may involvedelivering with a first chimp vector of the invention followed byboosting with a second chimp vector, or with a composition containingthe antigen itself in protein form. In one example, the prime-boostregimen can provide a protective immune response to the virus, bacteriaor other organism from which the antigen is derived. In another desiredembodiment, the prime-boost regimen provides a therapeutic effect thatcan be measured using convention assays for detection of the presence ofthe condition for which therapy is being administered.

The priming composition may be administered at various sites in the bodyin a dose dependent manner, which depends on the antigen to which thedesired immune response is being targeted. The invention is not limitedto the amount or situs of injection(s) or to the pharmaceutical carrier.Rather, the regimen may involve a priming and/or boosting step, each ofwhich may include a single dose or dosage that is administered hourly,daily, weekly or monthly, or yearly. As an example, the mammals mayreceive one or two doses containing between about 10 μg to about 50 μgof plasmid in carrier. A desirable amount of a DNA composition rangesbetween about 1 μg to about 10,000 μg of the DNA vector. Dosages mayvary from about 1 μg to 1000 μg DNA per kg of subject body weight. Theamount or site of delivery is desirably selected based upon the identityand condition of the mammal.

The dosage unit of the vector suitable for delivery of the antigen tothe mammal is described herein. The vector is prepared foradministration by being suspended or dissolved in a pharmaceutically orphysiologically acceptable carrier such as isotonic saline; isotonicsalts solution or other formulations that will be apparent to thoseskilled in such administration. The appropriate carrier will be evidentto those skilled in the art and will depend in large part upon the routeof administration. The compositions of the invention may be administeredto a mammal according to the routes described above, in a sustainedrelease formulation using a biodegradable biocompatible polymer, or byon-site delivery using micelles, gels and liposomes. Optionally, thepriming step of this invention also includes administering with thepriming composition, a suitable amount of an adjuvant, such as aredefined herein.

Preferably, a boosting composition is administered about 2 to about 27weeks after administering the priming composition to the mammaliansubject. The administration of the boosting composition is accomplishedusing an effective amount of a boosting composition containing orcapable of delivering the same antigen as administered by the primingDNA vaccine. The boosting composition may be composed of a recombinantviral vector derived from the same viral source (e.g., adenoviralsequences of the invention) or from another source. Alternatively, the“boosting composition” can be a composition containing the same antigenas encoded in the priming DNA vaccine, but in the form of a protein orpeptide, which composition induces an immune response in the host. Inanother embodiment, the boosting composition contains a DNA sequenceencoding the antigen under the control of a regulatory sequencedirecting its expression in a mammalian cell, e.g., vectors such aswell-known bacterial or viral vectors. The primary requirements of theboosting composition are that the antigen of the composition is the sameantigen, or a cross-reactive antigen, as that encoded by the primingcomposition.

In another embodiment, the simian adenoviral vectors of the inventionare also well suited for use in a variety of other immunization andtherapeutic regimens. Such regimens may involve delivery of simianadenoviral vectors of the invention simultaneously or sequentially withAd vectors of different serotype capsids, regimens in which adenoviralvectors of the invention are delivered simultaneously or sequentiallywith non-Ad vectors, regimens in which the adenoviral vectors of theinvention are delivered simultaneously or sequentially with proteins,peptides, and/or other biologically useful therapeutic or immunogeniccompounds. Such uses will be readily apparent to one of skill in theart.

The following examples illustrate the cloning of the simian adenovirusesand the construction of exemplary recombinant adenovirus vectors of thepresent invention. These examples are illustrative only, and do notlimit the scope of the present invention.

Example 1 Viral Propagation

The Pan5 [ATCC Accession No. VR-591], Pan6 [ATCC Accession No. VR-592],and Pan7 [ATCC Accession No. VR-593] viruses, originally isolated fromlymph nodes from chimpanzees, were propagated in 293 cells [ATCCCRL1573]. Typically, these cells are cultured in Dulbecco's ModifiedEagles Medium (DMEM; Sigma, St. Louis, Mo.) supplemented with 10% fetalcalf serum (FCS) [Sigma or Hyclone, Logan, Utah] and 1%Penicillin-Streptomycin (Sigma). Infection of 293 cells is carried outin DMEM supplemented with 2% FCS for the first 24 hours, after which FCSis added to bring the final concentration to 10%. Infected cells areharvested when 100% of the cells exhibit virus-induced cytopathic effect(CPE), and are then collected, and concentrated by centrifugation. Cellpellets are resuspended in 10 mM Tris (pH 8.0), and lysed by 3 cycles offreezing and thawing. Virus preparations are obtained following twoultra centrifugation steps on cesium chloride density gradients andstocks of virus are diluted to 1 to 5×10¹² particles/ml in 10 mMTris/100 mM NaCl/50% glycerol and stored at −70° C.

The ability of 293 cells to propagate these adenoviruses exceededexpectations which were based on knowledge of other non-human adenovirusserotypes.

Virus Yield (virus particles produced in 8 × 10⁸ cells) Pan5 8.8 × 10¹³Pan6 1.6 × 10¹⁴ Pan7 8.8 × 10¹³

Example 2 Characterization of Viral Genomic DNA

Genomic DNA was isolated from the purified virus preparations of Example1 and digested with HindIII or BamHI restriction enzymes following themanufacturers' recommendations. The results (not shown) revealed thatthat the Pan5, Pan6, Pan7 genomes of the invention and the published Pan9 (C68) genome show different restriction patterns, and thus, aredistinct from each other.

The nucleotide sequences of Pan5, Pan6 and Pan7 were determined. Thenucleotide sequence of the top strand of Pan5 DNA is reported in SEQ IDNO: 1. The nucleotide sequence of the top strand of Pan6 DNA is reportedin SEQ ID NO: 5. The nucleotide sequence of the top strand of Pan7 DNAis reported in SEQ ID NO: 9.

Regulatory and coding regions in the viral DNA sequences were identifiedby homology to known adenoviral sequences using the “Clustal W” programdescribed above at conventional settings. See the tables above providingthe adenoviral sequences. Open reading frames were translated and thepredicted amino acid sequences examined for homology to previouslydescribed adenoviral protein sequences, Ad4, Ad5, Ad7, Ad12, and Ad40.

Analysis of the sequence revealed a genome organization that is similarto that present in human adenoviruses, with the greatest similarity tohuman Ad4. However, substantial differences in the hexon hypervariableregions were noted between the chimpanzee adenoviruses and other knownadenoviruses, including AdHu4. These differences fit well with theserological cross-reactivity data that has been obtained (see below).

An alignment of a portion of the hexon sequences is shown in FIG. 1. Theportion shown is from the region of the hexon that corresponds to theoutwardly disposed extended loops DE1 and FG1 where the most variabilitybetween serotypes is observed. An intervening portion that contributesto the base of the hexon (corresponding to residues 308-368 of thepublished AdC68 sequence; U.S. Pat. No. 6,083,716), and is highlyconserved between serotypes, is also present. The following tablesummarizes the pair-wise comparisons of the amino acids in the hexonproteins.

Hexon amino- Comparison acid #1 #2 Similarity (%) AdC5 AdC7 99.0 AdC5AdC68 98.3 AdC5 AdC6 88.0 AdC5 AdC1 84.9 AdC6 AdC7 87.7 AdC6 AdC68 87.3AdC6 AdC1 84.9 AdC7 AdC68 97.5 AdC7 AdC1 84.8 AdC68 AdC1 84.9

Analysis of the fiber knob domain (which is responsible for receptorbinding) of the chimpanzee adenoviruses shows an overall similarity instructure (FIG. 2).

The degree of sequence similarity between the E1 proteins of huAd5 andC68 (see Tables below) is similar to that between huAd5 and Pan-5,Pan-6, and Pan-7.

E1a (13S) Comparison amino-acid #1 #2 identity (%) AdHu5 AdC5 36.6 AdHu5AdC6 28.5 AdHu5 AdC7 34.9 AdHu5 AdC68 35.6 AdHu5 AdC1 35.6 AdC5 AdC668.3 AdC5 AdC7 96.9 AdC5 AdC68 80.4 AdC5 AdC1 51.3 AdC6 AdC7 69.3 AdC6AdC68 59.4 AdC6 AdC1 37.7 AdC7 AdC68 81.5 AdC7 AdC1 51.0 AdC68 AdC1 54.9

Sequence Identity with human Ad5 E1b Small T E1b Large T Protein ProteinC68 47.3% 55.8% Pan-5 43.2% 54.5% Pan-6 45.3% 54.5% Pan-7 46.4% 53.8%

Replication-defective versions of AdC5, AdC6 and AdC7 were created bymolecular cloning methods described in the following examples in whichminigene cassettes were inserted into the place of the E1a and E1bgenes. The molecular clones of the recombinant viruses were rescued andgrown up in 293 cells for large-scale purification using the publishedCsCl sedimentation method [K. Fisher et al., J. Virol., 70:520 (1996)].Vector yields were based on 50 plate (150 mm) preps in whichapproximately 1×10⁹ 293 cells were infected with the correspondingviruses. Yields were determined by measuring viral particleconcentrations spectrophotometrically. After having constructedE1-deleted vectors, it was determined that HEK 293 cells (which expresshuman adenovirus serotype 5 E1 functions) trans-complement the E1deletions of the novel viral vectors and allow for the production ofhigh titer stocks. Examples of virus yields for a few of theserecombinant viruses are shown in the table below.

The transgenes for these vectors, β-galactosidase (LacZ), greenfluorescent protein (GFP), alpha-1-anti-trypsin (A1AT), ebolaglycoprotein (ebo), a soluble ebola glycoprotein variant lacking thetransmembrane and cytoplasmic domains (sEbo), and three deletion mutantsof the ebola glycoprotein (EboΔ2, EboΔ3, and EboΔ4), were expressed bythe cytomegalovirus promoter (CMV). In the following table, ND indicatesthat the study has not yet been done.

Viral backbone/Vector yield (Viral particles × 10¹³) Transgene AdHu5AdC7 AdC68 AdC6 CMVLacZ 1.5 1.4 3.3 6.1 CMVGFP 2.5 3.6 8 10 CMVA1AT 3.76 10 ND CMVEbo 1.1 4.3 ND ND CMVsEbo 4.9 5.4 ND ND CMVEboΔ2 1 9.3 ND NDCMVEboΔ3 0.8 9.5 ND ND CMVEboΔ4 1.4 6.2 ND ND

The ability of human adenovirus E1 to trans-complement the E1-deletedchimpanzee viruses of the invention is highly advantageous, as itpermits the production of E1-deleted chimpanzee adenoviral vectors ofthe invention, while reducing or eliminating the risk of homologousrecombination due to the differences in sequences between human Ad andthe chimpanzee adenoviruses described herein.

Example 3 Serological Studies of Pan 5, 6, and 7 Viruses

Because of the differences in the hexon hypervariable region, it wasanticipated that the C5, C6, and C7 viruses would be serologicallydistinct from human adenoviruses, including AdHu4.

1. Cross-Reactivity of Wild-Type Viruses

For screening of wild-type viruses in order to make a determination ofantibody cross-reactivity, the replication competent viruses were usedand inhibition of cytopathic effects (CPE) was measured. Briefly,preparations of adenoviruses (Adhu5, Pan-5, Pan-6, Pan-7 and AdC68)stored at 5×10¹² particles/ml were diluted 1/600 for the assays. Thisconcentration of virus was selected since it results in 100% CPE within48 hours in the absence of neutralization. Prior to adding the virus to293 cells (4×10⁴ cells/well in a 96 well dish), 1:20 dilutions of serawere added. The assay is read as the presence or absence of CPE; fullneutralization would read as no cytopathic effect. The results aresummarized in the Table below. The fact that 9/36 human sera neutralizedAdhu5 induced CPE is consistent with previous estimates of neutralizingantibodies in the human population. The numbers indicate the totalindividuals who showed neutralization (numerator) versus the totalnumber screened (denominator). ND=not determined

Neutralization by 1/20 diln of serum Human Rhesus Chimpanzee (N = 36) (N= 52) (N = 20) Adhu5 9/36 ND ND AdC68 1/36 0/52 12/20 Pan 5 0/36 0/5210/20 Pan 6 0/36 0/52  9/20 Pan 7 0/36 0/52 12/20

Of all human sera screened, 35/36 were negative for neutralization toAdC68 while 36/36 were negative for neutralization to Pan-5, Pan-6 andPan-7. Of 52 rhesus monkeys screened, none showed neutralization to anychimpanzee adenovirus; rhesus monkey is the preferred pre-clinical modelfor evaluating HIV vaccines. Between 9 to 12 out of 20 chimpanzees hadsubstantial neutralization to one or another of the chimpanzeeadenoviruses consistent with the fact these are indeed endemicchimpanzee-specific pathogens. Interestingly, there are chimpanzees withneutralizing antibodies only to Pan-5, Pan-6 or AdC68 supporting thehypothesis that several of these chimpanzee adenoviral vectors will notcross neutralize each other and are distinct serotypes.

The same assay was carried out for 20 chimpanzee serum samples. Fiftypercent (50%) of the samples reacted serologically, in different degreesto Pan5; 40% to Pan6; 55% to Pan7 and 60% to C68. Among the positiveserum samples, one of them had strong neutralizing activity to all fourchimp viruses.

2. Cross-Neutralization with Recombinant Viruses

High-titer polyclonal antibodies were obtained to each of the simianadenoviruses in order to more precisely gauge the degree ofcross-neutralization among the different serotypes. This was done byintramuscular immunization of rabbits using a recombinant viruscontaining GFP based on previously the described C68 chimpanzeeadenovirus as an adjuvant. The serum was then used to assay forneutralizing activity against each of the three chimpanzee adenovirusesof the invention, AdC5, AdC6 and AdC7. A rabbit was injected with 5×10¹²viral particle per kg of C68CMVGFP vector intramuscularly and boosted 5weeks later using the same dose. A bleed collected at the 9 week timepoint revealed extremely potent neutralizing activity against C68 aswell as Pan-5 and Pan-7 but not against Pan-6 (see Table below),indicating that the administration of a C68 (or Pan-5 and Pan-7) basedvaccine could be effectively followed by a boost using a vector based onPan-6. However, it has been found that this level of inter-relatednessdoes not necessarily prevent with re-administration in a setting whereantiviral antibody titers were not as high as was achieved in thisrabbit. In the following table, + indicates 33% CPE; ++ indicates 66%CPE; +++ indicates 100% CPE.

Infection on 293 cells with virus: C68 Serum Pan5 Pan6 Pan7 Pan9(C68)GFP Dilution − +++ − − − 1/20 − +++ − − − 1/40 − +++ − − − 1/80 − +++ −− − 1/160 − +++ − − − 1/320 − +++ − − − 1/640 − +++ − − − 1/1,280 − +++− − − 1/2,560 − +++ − − − 1/5,120 + +++ − − − 1/10,240 + +++ ++ − −1/20,480 ++ +++ +++ − − 1/40,960 ++ +++ +++ + + 1/81,920 +++ +++ +++ ++++ 1/163,840 +++ +++ +++ +++ +++ 1/327,680 +++ +++ +++ +++ +++ 1/665,360+++ +++ +++ +++ +++ 1/1,310,720 +++ +++ +++ +++ +++ 1/2,621,440

3. Quantitative Assay for Detection of Neutralizing Antibody

The result was validated by a more quantitative-based assay fordetecting neutralizing antibody, which is based on transduction of a GFPvector. Briefly, groups of C57BL/6 mice were immunized intramuscularlyor intravenously with 5.0×10¹⁰ particles/ml Pan5, Pan6, Pan7 or C68.Sera from day 28 bleeds were tested for cross-neutralizing activityagainst C68CMVEGFP at dilutions of 1/20 and 1/80. In summary, when apharmaceutical preparation of human immunoglobulin was tested forserological reactions to Pan 5, 6, and 7, and C68, some low levels ofneutralizing activities against Pan 7 and C68 were detected. Noneutralizing activity against Pan5 or Pan6 was detected. Serum samplesfrom 36 human subjects were run for the same assay. Serum samples weretested at a 1/20 dilution. The results indicated that only oneindividual has clear neutralizing activity to C68. No neutralizingactivity to Pan5, Pan6 or Pan7 was detected.

4. In Vitro Cross-Neutralization

Cross-neutralization of the simian adenoviruses by high-titer rabbitpolyclonal antibodies raised against each of the adenoviruses Pan-5,Pan-6, Pan-7, and C68 was tested.

Rabbits were immunized with intra-muscular injections of 10¹³ particlesof each of the chimpanzee adenoviruses and boosted 40 days later withthe same dose with incomplete Freund's adjuvant. Sera were analyzed orthe presence of neutralizing antibodies by incubating serial two-folddilutions with 10⁹ genome copies of each of the appropriate chimpanzeeadenovirus vector expressing GFP and testing for the attenuation of GFPexpression when applied to 293 cells. The serum dilution which produceda 50% reduction of GFP expression was scored as the neutralizingantibody titer against that particular virus.

The results are shown in the Table. The data are consistent with theexpectation from sequence analysis of the hexon amino-acid sequences,which indicated that Ad Pan-6 was likely to be the most serologicallydistinct compared to the other chimpanzee adenoviruses.

Serum from rabbit immunized Infection of 293 cells with 10⁹ genomecopies of with: Ad Pan-5 Ad Pan-6 Ad Pan-7 Ad C68 Ad Pan-5 1/5120 <1/20 1/2560  1/2560 Ad Pan-6 No  1/20,480 <1/20 <1/20 neutralization AdPan-7 1/2560  1/160  1/163,840  1/2560 Ad C68 No <1/20 <1/20  1/5120neutralization

In order to determine whether antibodies cross-reacting with the simianadenoviruses were likely to be of low prevalence in humans, simianadenoviruses SV1, SV39, and SV25 were tested for their ability towithstand neutralization when incubated with commercially availablepooled human immunoglobulins (Ig). The same assay was also performedwith Adhu5 and the chimpanzee adenoviruses Pan-5, Pan-6, Pan-7, and C68.In a further study, sera from mice has been immunized with one of thechimpanzee adenoviruses C5, C6, C7, and C68 and their ability tocross-neutralize the simian adenoviruses SV-15, SV-23, SA-17, and BaboonAdenovirus has been tested. No cross-reactivity was observed in anycase.

Example 4 Generation of Recombinant E1-Deleted Pan5 Vector

A modified pX plasmid was prepared by destroying the FspI site in thebla gene region of pX (Clontech) by site-directed mutagenesis. Theresulting modified plasmid, termed pX′, is a circular plasmid of 3000 bpwhich contains an f1 ori and an ampicillin resistance gene (AmpR-cds).

A. Production of Pan-5 Adenovirus Plasmid

A polylinker for sequential cloning of the Pan5 DNA fragments into pX′is created. The polylinker is substituted for the existing pX′polylinker following digestion with MiuI and EcoRI. The blunt-FseIfragment of the Pan 5 is inserted into the SmaI and FseI sites of thepolylinker. This fragment contains the 5′ end of the adenoviral genome(bp 1 to 3606, SEQ ID NO:1). The SnaBI-FspI fragment of Pan 5 (bp 455 to3484, SEQ ID NO:1) is replaced with a short sequence flanked by I-Ceuand PI-Sce sites from pShuttle (Clontech), to eliminate the E1 region ofthe adenoviral genome. The EcoRI-blunt fragment of Pan5 (bp 28658 to36462, SEQ ID NO:1) is inserted into the EcoRI and EcoRV sites of thepolylinker (to provide the 3′ end of the adenoviral genome); theFseI-MluI fragment (bp 3606 to 15135, SEQ ID NO:1) is inserted into thepolylinker; and the MluI-EcoRI fragment is inserted into the polylinker(bp 15135 to 28658, SEQ ID NO:1). Optionally, a desired transgene isinserted into I-CeuI and PI-SceI sites of the newly created pX′Pan5)E1vector.

B. Alternative Method of Generating pX′Pan5)E1.

The initial plasmid pX is derived from pAdX adenovirus plasmid availablefrom Clontech, as described above. Thereafter, a PacI-XhoI region of pX′was deleted and the blunt-ended Pan5 polylinker was inserted into theFspI site to generate pX′PLNK (2994 bp). The 5′end-FseI region of Pan 5(bp 1-3607, SEQ ID NO:1) was inserted into SmaI and FseI sites of pX′LNKto generate the pX′Pan5-5′ plasmid (6591 bp). The SnaBi-NdeI region ofpX′Pan5-5′ was excised and replaced with the Ceu/Sce cassette, which hadbeen PCR amplified from pRCS to create pX′Pan5-5′)E1 (4374 bp). Briefly,a sequence containing I-CeuI and PI-SceI rare cutter sites was PCRamplified from pRCS (3113 bp). The 3′ PCR primer was introduced an NdeIsite into the PCR product.

To extend the Pan5 DNA in pX′Pan5-5′)E1 (4374 bp), the FseI-MluI regionof Pan 5 (bp 3607-15135, SEQ ID NO:1) is added, to create pX′Pan5-5′Mlu(15900 bp). The remaining MluI-3′ end of the Pan5 sequence (bp15135-36462, SEQ ID NO:1) is added to the vector between the MluI andEcoRV sites of the vector polylinker to form pX′Pan5)E1 which containsthe full-length Pan5 sequence containing a deletion in the E1 region.

C. Generation of Recombinant Viruses

To generate the recombinant adenoviruses from pX′Pan5)E1, the plasmid isco-transfected with a helper expressing E1, or from an E1-expressingpackaging cell line, such as 293 cell line or a cell line prepared asdescribed herein. The expression of E1 in the packaging cell permits thereplication and packaging of the Pan5)E1 into a virion capsid. Inanother embodiment, the packaging cell transfected with pX′Pan5)E1 istransfected with an adenovirus vector as described above bearing thetransgene of interest. Homologous recombination occurs between thehelper and the plasmid, which permits the adenovirus-transgene sequencesin the vector to be replicated and packaged into virion capsids,resulting in the recombinant adenovirus.

Transfection is followed by an agar overlay for 2 weeks, after which theviruses are plagued, expanded and screened for expression of thetransgene. Several additional rounds of plaque purification are followedby another expansion of the cultures. Finally the cells are harvested, avirus extract prepared and the recombinant chimpanzee adenoviruscontaining the desired transgene is purified by buoyant densityultracentrifugation in a CsCl gradient or by alternative means known tothose of skill in the art.

Example 5 Generation of Recombinant E1-Deleted Pan6 Vector

A. Strategy for Construction of Pan-6 Adenoviral Plasmid

1. Cloning of Terminal Fragments

Pan 6 virus is deproteinated by pronase and proteanase K treatment andphenol extraction. Synthetic 12 bp Pme I linkers are ligated onto theviral DNA as described by Berkner and Sharp, Nucleic Acids Research, 11:6003 (1983). The viral DNA is then digested with Xba I to isolate a 5′terminal fragment (6043 bp). The Ad6 XbaI 5′ fragment is then ligatedinto pX link at Sma I and Xba I sites to form pX-AdPan6-0-16.5. Theviral DNA with Pme I linkers is also digested with Pac I to isolate the6475 bp 3′ terminal fragment and cloned into pX link at Pac I and Sma Isites, resulting in pXAdPan6-82-100.

2. Deletion of E1 from the 5′ Clone

To delete E1 (m.u.1.2-9), the BsiWi-Xba I fragment in pX-AdPan6-0-16.5is replaced with a PCR fragment spanning m.u.9-16.7 fragment treatedwith BsiWi and Xba I, leading to pX-Ad-Pan6 m.u.0-1, 9-16.5.

3. Fusion of 5′ and 3′ Clones and to Create an Anchor Site to Accept theMiddle Hind III Fragment

First, the 5′ clone, pX-Ad-Pan6 m.u.0-1, 9-16.5, is further expanded byinserting the 2^(nd) Xba I fragment (4350 bp, m.u.16.5-28) from Pan 6genome into the Xba I site in the pX-Ad-Pan6 m.u.0-1, 9-16.5. Thisconstruct is named pXAd-Pan6-mu 0-1, 9-28.

Second, the 3′ clone is also expanded by inserting the 15026 bp MluI/Pac I fragment covering m.u.41-82 from Pan 6 genome into the Mlu I/PacI sites of pXAdPan6-82-100, generating pXAdPan6-m.u.41-100.

Then, a 8167 bp Hind III/Eco 47111 Pan 6 fragment is isolated frompXAd-Pan6-mu 0-1, 9-28 and subcloned into pXAdPan6-m.u.41-100 at HindIII and Xba I blunt sites. This 5′ and 3′ fusion clone is calledpXAdPan6mu0-1, 9-19.5, 64-100.

4. Drop of the Middle Fragment of the Genome into the Fusion Clone

A 16335 bp Hind III fragment (m.u.19.5-64) from Pan 6 is inserted intoHind III site of pXAdPan6mu0-1, 9-19.5, 64-100 to form pXAdPan6-0-1,9-100.

5. Introduction of a PKGFP Selective Marker into the Final Construct forDirect Cloning the Gene of Interest and Green/White Selection ofRecombinant Transformants.

A minigene cassette that expresses GFP under a lac promoter and isflanked with recognition sites of rare intron encoding restrictionenzymes, PI-Sce I and I-Ceu I, was isolated from pShuttle-pkGFP (bare)by Sap I and Dra III digestions followed by filling-in reaction. ThepShuttle-pkGFP (bare) plasmid is 4126 bp in length, and contains aColE1-Ori, a kanamycin resistance gene, plac, a LacZ promoter-GFPmut3-1cds (Clontech), and a GFPmut3-1 cds (Clontech). This cassette issubcloned into Srf I cut and blunted pXAdPan6-0-1, 9-100. This finalconstruct is called pX-Pan6-pkGFP mu.0-1, 9-100, which is useful forgenerating recombinant E1-deleted Pan 6 molecular clones carrying genesof interest by direct ligation and green/white selection in combinationwith the generic pShuttlepkGFP vectors.

B. Alternative Strategy for Generation of Pan-6 Plasmid

1. Cloning of 5′ Terminal Fragment

The Pan 6 virus is deproteinated by pronase and proteanase K treatmentand phenol extraction as described above and synthetic 12 bp Pme Ilinkers are ligated onto the viral DNA as described. The AdPan6 5′ XbaIfragment is isolated and ligated into pX to form pX-AdPan6-0-16.5 (9022bp) as described in Part A above.

2. Deletion of E1 from the 5′ Clone

To delete E1 (m.u. 1.2-9), pX-AdPan6-0-16.5 is digested with SnaBI andNdeI to remove the regions encoding the E1a and E1b proteins (3442-6310bp). This vector is subsequently digested with BsiWI in preparation forblunting with the minigene cassette carrying a selective marker.

3. Introduction of a Selective Marker

A minigene cassette that expressed GFP under a lac promoter and which isflanked with recognition sites of rare intron encoding restrictionenzymes, PI-XceI and I-CeuI, was isolated from pShuttle-pkGFP asdescribed above. The DraIII-SapI fragment is then ligated with thedigested pX-AdPan6-0-16.5 to form pX-AdPan6 MU 0-16.5)E1 (7749 bp).

4. Extension of Pan-6 Adenoviral Sequences

pX-AdPan6 MU 0-16.5)E1 was subjected to XbaI digestion to permitinsertion of an XbaI-RsrII linker. An XbaI/RsrII digestion fragment fromthe AdPan6 genome was isolated (mu 28-100, 26240 bp) and ligated intothe Xba/RsrII-digested pX-AdPan6 MU 0-16.5)E1 to provide pX-AdPan6 MU0-1, 9-16.5, 28-100. A second XbaI fragment from the Pan6 genome (mu16.5-28, 4350 bp) is then ligated into this plasmid to form pX-AdPan6 MU0-1, 9-100 (38551 bp).

C. Generation of Recombinant Adenoviruses

To generate the recombinant adenoviruses from a E1-deleted Pan6 plasmidprepared as described in Parts A or b, the plasmid is co-transfectedwith a helper expressing E1, or from an E1-expressing packaging cellline, such as 293 cell line or a cell line prepared as described herein.The expression of E1 in the packaging cell permits the replication andpackaging of the Pan6-pkGFP mu.0-1, 9-100 into a virion capsid.Alternatively, the packaging cell transfected with pX-Pan6-pkGFP mu.0-1,9-100 is transfected with an adenovirus vector as described abovebearing another transgene of interest.

Example 6 Generation of Recombinant E1-Deleted Pan7 Vector

A. Generation of Pan7 Plasmids

A synthetic linker containing the restriction sitesPacI-SmaI-FseI-MluI-EcoRV-PacI was cloned into pBR322 that was cut withEcoRI and NdeI. The left end (bp1 to 3618) of Ad Pan7 was cloned intothe linker between the SmaI and FseI sites. The adenovirus E1 was thenexcised from the cloned left end by cutting with SnaBI and NdeI andinserting an I-CeuI-GFP-PI-SceI cassette from pShuttle (Clontech) in itsplace. The resulting plasmid was cut with FseI and MluI and Ad Pan7fragment FseI (bp 3618) to MluI (bp 155114 was inserted to extend theleft end. The construct (pPan7pGFP) was completed by inserting the 21421bp Ad Pan7 right end fragment from the MluI site (bp 15114) into theabove plasmid between MluI and EcoRV to generate a complete molecularclone of E1 deleted adenovirus Pan7 suitable for the generation ofrecombinant adenoviruses. Optionally, a desired transgene is insertedinto the I-CeuI and PI-SceI sites of the newly created pPan7 vectorplasmid.

B. Construction of E1-Deleted Pan7 Viral Vectors

To generate the recombinant adenoviruses from pPan7)E1, the plasmid isco-transfected with a helper expressing E1, or from an E1-expressingpackaging cell line, such as 293 cell line or a cell line prepared asdescribed herein. The expression of E1 in the packaging cell permits thereplication and packaging of the Pan7)E1 into a virion capsid. Inanother embodiment, the packaging cell transfected with pX′Pan7)E1 istransfected with an adenovirus vector as described above bearing thetransgene of interest. Homologous recombination occurs between thehelper and the plasmid, which permits the adenovirus-transgene sequencesin the vector to be replicated and packaged into virion capsids,resulting in the recombinant adenovirus. Transfection and purificationis as described above.

Example 7 Generation of Plasmid Vectors Expressing the E1 Genes

Plasmid vectors are constructed which encode the Pan5 E1 region gene,and these plasmids are used to generate stable cell lines expressingviral E1 proteins.

The E1 region of Pan5 is cloned into pX′, essentially as described inExample 4 above, prior to replacement of this region with the fragmentfrom pShuttle (Clontech). The expression plasmid contains the Pan5adenoviral genome sequence spanning at least by 1 to 3959 in the Pan5genomic sequence. Thus, the expression plasmid contains the sequenceencoding E1a and E1b of chimpanzee Ad Pan5 under the control of aheterologous promoter. Similar expression plasmids can be generatedusing the Ad Pan6 and AdPan 7 E1 regions, identified in the tablesabove.

Example 8 Generation of Cell Lines Expressing Chimpanzee Adenovirus E1Proteins

Cell lines expressing viral E1 proteins are generated by transfectingHeLa (ATCC Acc. No. CCL2) with the plasmid of Example 6. These celllines are useful for the production of E1-deleted recombinant chimpanzeeadenoviruses by co-transfection of genomic viral DNA and the expressionplasmids described above. Transfection of these cell lines, as well asisolation and purification of recombinant chimpanzee adenovirusestherefrom are performed by methods conventional for other adenoviruses,i.e., human adenoviruses [see, e.g., Horwitz, cited above and otherstandard texts].

A. Cell Lines Expressing Pan5 E1 Proteins

HeLa cells in 10 cm dishes are transfected with 10 μg of pX-Pan51-E1 DNAusing a Cellphect™ kit (Pharmacia, Uppsala, Sweden) and following themanufacturer's protocol. 22 hours post-transfection, the cells aresubjected to a three minute glycerol shock (15% glycerol in HepesBuffered Saline, pH 7.5) washed once in DMEM (HeLa) or F12K (A549; LifeTechnologies, Inc., Grand Island, N.Y.) media supplemented with 10% FCS,1% Pen-Strep, then incubated for six hours at 37° C. in the abovedescribed media. The transfected cells are then split into duplicate 15cm plates at ratios of 1:20, 1:40, 1:80, 1:160, and 1:320. Followingincubation at 37° C. overnight, the media is supplemented with G418(Life Technologies, Inc.) at a concentration of 1 μg/ml. The media isreplaced every 5 days and clones are isolated 20 days post-transfection.

HeLa E1 cell clones are isolated and assayed for their ability toaugment adeno-associated virus (AAV) infection and expression ofrecombinant LacZ protein as described below.

B. AAV Augmentation Assay for Screening E1 Expressing Cell Lines

AAV requires adenovirus-encoded proteins in order to complete its lifecycle. The adenoviral E1 proteins as well as the E4 region-encoded ORF6protein are necessary for the augmentation of AAV infection. An assayfor E1 expression based on AAV augmentation is used. Briefly, the methodfor identifying adenoviral E1-expressing cells comprises the steps ofinfecting in separate cultures a putative adenovirus E1-expressing celland a cell containing no adenovirus sequence, with both anadeno-associated virus (AAV) expressing a marker gene and an AAVexpressing the ORF6 of the E4 gene of human adenovirus, for a suitabletime. The marker gene activity in the resulting cells is measured andthose cells with significantly greater measurable marker activity thanthe control cells are selected as confirmed E1-expressing cells. In thefollowing experiment, the marker gene is a lacZ gene and the markeractivity is the appearance of blue stain.

For example, the cell lines described above, as well as untransfectedcontrol cells (HeLa) are infected with 100 genomes per cell of an AAVvector bearing a marker gene, e.g., AV.LacZ [K. Fisher et al., J.Virol., 70:520 (1996)] and an AAV vector expressing the ORF6 region ofhuman 5 (AV.orf6). The DNA sequence of the plasmid generates a novelrecombinant adeno-associated virus (rAAV) containing the LacZ transgeneand the Ad E4 ORF 6, which is an open reading frame whose expressionproduct facilitates single-stranded (ss) to double-stranded (ds)conversion of rAAV genomic DNA. These vectors are incubated in mediumcontaining 2% FCS and 1% Pen-Strep at 37° C. for 4 hours, at which pointan equal volume of medium containing 10% FCS is added. It should beunderstood by one of skill in the art that any marker gene (or reportergene) may be employed in the first AAV vector of this assay, e.g.,alkaline phosphatase, luciferase, and others. An antibody-enzyme assaycan also be used to quantitate levels of antigen, where the markerexpresses an antigen. The assay is not limited by the identity of themarker gene. Twenty to twenty-four hours post-infection, the cells arestained for LacZ activity using standard methods. After 4 hours thecells are observed microscopically and cell lines with significantlymore blue cells than the A549 or HeLa cell controls are scored aspositive.

Example 9 Delivery of Transgene to Host Cell

The resulting recombinant chimpanzee adenovirus described in Example 4,5 or 6 above is then employed to deliver the transgene to a mammalian,preferably human, cell. For example, following purification of therecombinant virus, human embryonic kidney 293 cells are infected at anMOI of 50 particles per cell. GFP expression was documented 24 hourspost-infection.

A. Gene Transfer in Mouse Models Via Pan-6, Pan-7, and Pan-9 Vectors

Gene transfer efficiencies and toxicological profile of recombinantchimpanzee adenoviruses were compared in mouse liver directed genetransfer, mouse lung directed gene transfer, and mouse muscle directedgene transfer.

E1-deleted adenoviral vectors containing LacZ under the control of theCMV promoter were constructed using the techniques herein for human Ad5,chimpanzee Pan 6, chimpanzee Pan 7 and chimpanzee Pan 9 (C68). Thevectors were delivered to immune-deficient NCR nude mice (80 for eachstudy) as follows. For the liver study, 100 μl (1×10¹¹ particles) wereinjected into the tail vein. For the lung study, 50 μl (5×10¹⁰particles) were delivered intratracheally. For the muscle study, 25 μl(5×10¹⁰ particles) were injected into tibialis anterior. The mice weresacrificed on days 3, 7, 14 and 28 post-vector injection (5 animals pergroup at each time point). At each necropsy, the liver/lung/muscletissue was harvested and prepared for cryoblocks and paraffin embedding.The cryoblocks were sectioned for X-gal staining and the paraffinsections are H&E stained for histopathic analysis. At each time point,terminal bleeding was performed. Serum samples were subjected to liverfunction tests.

It was observed in this experiment the chimpanzee adenoviruses Pan-6,Pan-7, and Pan-9 were less efficient than huAd5 in gene transfer to theliver and to the lung. However, this may be desirable in certaincircumstances, to reduce liver toxicity observed for huAd5. The genetransfer efficiency in muscle varied less between serotypes.

B. Mouse Study to Feasibility of Re-Administration of Adenovirus Vectorsby Serotype Switching Between Adhu5, Pan-6, Pan-7, and Pan-9 Vectors

Mice were administered (C57/Bl6; 4/group) LacZ vectors based on huAd5,Pan-6, Pan-7, and Pan-9 (H5.040CMVLacZ, Pan6.000CMVLacZ,Pan7.000CMVLacZ, Pan9.000CMVLacZ; 10¹¹ particles/injection) by tailvein. Thirty days later the mice were re-administered adenovirus vectorsexpressing al-antitrypsin (H5.040CMVhA1AT, Pan6.000CMVhA1AT, 1×10¹¹particles, Pan7.000CMVhA1AT, Pan9.000CMVhA1AT, 10¹¹particles/injection). Successful transduction by the re-administeredvector is monitored by measuring serum al-antitrypsin on days 3 and 7,following re-administration.

The ability of adenovirus vectors based on huAd5, Pan-6, Pan-7, andPan-9 respectively to transduce the livers of mice in the presence ofneutralizing antibodies to the other serotypes was determined. Theresults are tabulated here.

1^(st) injection 2^(nd) injection Cross-neutralization Adhu5 Adhu5 Yes(+ve control) Pan-6 No Pan-7 No Pan-9 (C68) No Pan-6 Adhu5 No Pan-6 Yes(+ve control) Pan-7 Yes Pan-9 (C68) No Pan-7 Adhu5 No Pan-6 Yes Pan-7Yes (+ve control) Pan-9 (C68) Yes Pan-9 (C68) Adhu5 No Pan-6 No Pan-7Yes Pan-9 (C68) Yes (+ve control)

Ability of vectors to transduce murine liver in the presence ofneutralizing antibodies to other serotypes.

Thus, immunization with huAd5 does not prevent re-administration witheither of the chimpanzee adenovirus vectors Pan-6, Pan-7, or Pan-9(C68). This experiment also appears to indicate that Pan-7 is betweenPan-6 and Pan-9 in the spectrum of antigenic relatedness andcross-reacts with both; however Pan-6 and Pan-9 do not neutralize eachother. This is a surprising result based on homology comparisons, whichindicates that Pan-6 is quite distinct from Pan-7 and Pan-9. Evaluationof antisera generated against Pan-9 indicated no cross-neutralizationagainst Pan-6 but some neutralization against Pan-7, arguing that Pan-6is distinct from the others.

Example 10 Generation of Recombinant E1-Deleted SV-25 Vector

A plasmid was constructed containing the complete SV-25 genome exceptfor an engineered E1 deletion. At the site of the E1 deletionrecognition sites for the restriction enzymes I-CeuI and PI-SceI whichwould allow insertion of transgene from a shuttle plasmid where thetransgene expression cassette is flanked by these two enzyme recognitionsites were inserted.

A synthetic linker containing the restriction sitesSwaI-SnaBI-SpeI-AflII-EcoRV-SwaI was cloned into pBR322 that was cutwith EcoRI and NdeI. This was done by annealing together two syntheticoligomers SV25T (5′-AAT TTA AAT ACG TAG CGC ACT AGT CGC GCT AAG CGC GGATAT CAT TTA AA-3′, SEQ ID NO: 38) and SV25B (5′-TAT TTA AAT GAT ATC CGCGCT TAA GCG CGA CTA GTG CGC TAC GTA TTT A-3′, SEQ ID NO:39) andinserting it into pBR322 digested with EcoRI and NdeI. The left end (bp1to 1057, SEQ ID NO:29) of Ad SV25 was cloned into the above linkerbetween the SnaBI and SpeI sites. The right end (bp28059 to 31042, SEQID NO: 29) of Ad SV25 was cloned into the linker between the AflII andEcoRV sites. The adenovirus E1 was then excised between the EcoRI site(bp 547) to XhoI (bp 2031) from the cloned left end as follows. A PCRgenerated I-CeuI-PI-SceI cassette from pShuttle (Clontech) was insertedbetween the EcoRI and SpeI sites. The 10154 bp XhoI fragment of Ad SV-25(bp2031 to 12185, SEQ ID NO:29) was then inserted into the SpeI site.The resulting plasmid was digested with HindIII and the construct(pSV25) was completed by inserting the 18344 bp Ad SV-25 HindIIIfragment (bp11984 to 30328, SEQ ID NO:29) to generate a completemolecular clone of E1 deleted adenovirus SV25 suitable for thegeneration of recombinant adenoviruses. Optionally, a desired transgeneis inserted into the I-CeuI and PI-SceI sites of the newly created pSV25vector plasmid.

To generate an AdSV25 carrying a marker gene, a GFP (green fluorescentprotein) expression cassette previously cloned in the plasmid pShuttle(Clontech) was excised with the restriction enzymes I-CeuI and PI-SceIand ligated into pSV25 (or another of the Ad chimp plasmids describedherein) digested with the same enzymes. The resulting plasmid (pSV25GFP)was digested with SwaI to separate the bacterial plasmid backbone andtransfected into the E1 complementing cell line HEK 293. About 10 dayslater, a cytopathic effect was observed indicating the presence ofreplicative virus. The successful generation of an Ad SV25 basedadenoviral vector expressing GFP was confirmed by applying thesupernatant from the transfected culture on to fresh cell cultures. Thepresence of secondarily infected cells was determined by observation ofgreen fluorescence in a population of the cells.

Example 11 Construction of E3 Deleted Pan-5, Pan-6, Pan-7 and C68Vectors

In order to enhance the cloning capacity of the adenoviral vectors, theE3 region can be deleted because this region encodes genes that are notrequired for the propagation of the virus in culture. Towards this end,E3-deleted versions of Pan-5, Pan-6, Pan-7, and C68 have been made (a3.5 kb Nru-AvrII fragment containing E31-9 is deleted).

A. E3 Deleted Pan5 Based Vector

E1-deleted pPan5-pkGFP plasmid was treated with Avr II endonuclease toisolate a 5.8 kb fragment containing the E3 region and re-circulatepPan5-pkGFP with Avr II deletion to form construct pPan5-pkGFP-E3-AvrII. Subsequently, the 5.8 kb Avr II fragment was subcloned intopSL-Pan5-E3-Avr II for a further deletion of E3 region by Nru Idigestion. This led to a plasmid pSL-Pan5-E3-deletion. The finalconstruct pPan5-E3-pkGFP was produced by removing a 4.3 kb Avr II/Spe Ifragment from pSL-Pan5-E3-deletion plasmid and inserting intopPan5-pkGFP-E3-Avr II at Avr II site. In this final construct, a 3.1 kbdeletion in E3 region was accomplished.

B. E3 Deletion in Pan6 Based Vector

E1-deleted pPan6-pkGFP molecular clone was digested with Sbf I and Not Ito isolate 19.3 kb fragment and ligated back at Sbf I site. Theresulting construct pPan6-Sbf I-E3 was treated with Eco 47 III and SwaI, generating pPan6-E3. Finally, 21 kb Sbf I fragment from Sbf Idigestion of pPan6-pkGFP was subcloned into pPan6-E3 to createpPan6-E3-pkGFP with a 4 kb deletion in E3.

C. E3 Deleted Pan7 and Pan9 Vectors

The same strategy was used to achieve E3 deletions in both vectors.First, a 5.8 kb Avr II fragment spanning the E3 region was subclonedpSL-1180, followed by deletion of E3 bp Nru I digestion. The resultingplasmids were treated with Spe I and Avr II to obtain 4.4 kb fragmentsand clone into pPan7-pkGFP and pPan9-pkGFP at Avr II sites to replacethe original E3 containing Avr II fragments, respectively. The finalpPan7-E3-pkGFP and pPan9-E3-pkGFP constructs have 3.5 kb E3-deletions.

Example 12 Construction of E3- and E4-Deleted Pan-7 Vector

Although the deletion of the E1 region of adenoviruses (first generationadenovirus vectors) renders them replication-incompetent, expression ofthe adenoviral vector backbone genes is not fully abolished. Deletion ofthe E4 region considerably attenuates this residual gene expression andmay confer a safety advantage. An E4-deleted Pan-7 vector containing a2.5 kb deletion (a PvuII-AgeI fragment containing E4ORF1-ORF7 isdeleted) has been constructed. High titer stocks of this virus weregenerated using a HEK 293-based cell line, which in addition to E1,expresses an essential E4 gene (orf 6).

1. E4 Deletion in the Molecular Clone of Pan7

A 19 kb Xba I fragment was deleted from pPan7-pkGFP to create pPan7-XbaI from which a 2.5 kb E4 fragment was deleted by Age I and Pvu IIpartial digestion, resulting in pPan7-Xba I-E4. pPan7-E4-pkGFP plasmidwas generated from pPan7-Xba I-E4 in two sequential cloning steps,adding 19 kb Xba I and 15 kb I-Ceu I/Mlu I fragments, both of which camefrom pPan7-pkGFP construct.

2. Introduction of E3 and E4 Deletions in Pan9 Vector

A 11 kb plasmid, pPan9-EcoRI, containing E4 region was created byretrieving 11 kb EcoRI fragment from pPan9 pkGFP after EcoRI digestionand self-ligation. E4 region was deleted from this construct by Age Idigestion/filled in and Pvu II partial digestion and self-ligation togenerate pPan9-EcoR I-E4. A 23 kb EcoR I fragment was isolated frompPan9-pkGFP and inserted into pPan9-EcoR I-E4 at EcoR I site, followedby adding 5.8 kb Avr II fragment from pPan9-pkGFP, to form the finalproduct pPan9-E3-E4-pkGF. Compared to the genome size of wild type Pan9,this E1-E3-E4-deleted vector could have a transgene capacity up to 8 kb.

3. Introduction of Minigene Cassettes with Genes of Interest IncludingReporter Genes, Glyco- and Nuclear Proteins of Ebo into Molecular Clonesof Pan Vectors

A highly efficient direct cloning and green/white selection procedurewas employed for creating molecular clones of recombinant viruses.Briefly, genes of interest were cloned into pShuttlepkGFP by screeningwhite colonies for recombinants Subsequently, the minigene cassetteswere transferred into chimpanzee adenovirus backbone plasmids,pPanX-pkGFP with various deletions, easily by swapping with pkGFPcassette at I-Ceu I and PI-Sce I sites and screening a few whitecolonies for correct recombinants.

4. Rescue of Molecular Clones of Pan Vectors with Multiple Deletions inEarly Regions and Virus Propagation

For rescue of E1-E3-deleted molecular clones of chimpanzee adenovirusvectors, the clones were linearized with appropriate restriction enzymesand transfected into regular 293 cells. Once a full cytopathic effect(CPE) observed in the transfected cells, crude lysate was harvested andexpanded in 293 cells to large-scale infections. The viruses werepurified by CsCl sedimentation method.

For E1-E4 and E1-E3-E4-deleted Pan vectors, 10-3 cells, a 293-basedE1-E4-complementing cell line, were used for rescue and propagation ofvectors. E4 ORF6 gene expression in 10-3 cells was induced by additionof 150 μM ZnSO⁴ to the culture medium.

Example 13 Vaccination with Adenovirus Vectors Expressing Wild Type andVariant EboZ GP

AdHu5 or AdC7 vectors expressing Ebola envelope chimeras were producedfor in vivo immunization experiments in C57BL/6 mice. Recombinantviruses with different viral backbones were created by molecular cloningmethod in which the minigene cassettes were inserted into the place ofE1-deletions. The molecular clones of all recombinant viruses wererescued and grown up in 293 cells for large-scale purification usingCsCl sedimentation method. Five EboZ variants encoded by AdHu5 or AdPan7(C7) were selected and produced to evaluate their relativeimmunogenicity following an intramuscular Ad injection. The wt Ebo, asoluble Ebo variant, EboΔ1, EboΔ2, EboΔ3, EboΔ4, EboΔ5S, EboΔ6S, EboΔ7Sand EboΔ8S were evaluated in the initial vaccine studies. For the datasummarized in the following table, the number of viral particles (per mlor total) produced and amplified from infected 293 cells was establishedby spectrophotometry reading.

TABLE Production of Adhu5 or AdC7 Adenoviral vector encoding EboZvariant. HuAd5 AdC7 Total Total Titer yield Titer yield (VP x (VP x (VPx (VP x Gene 10¹²/ml) 10¹²) 10¹²/ml) 10¹²) Ebo wt 2.6 12 4.3 43 EboS 4.949 4.6 55 EboΔ2 2.1 9 5.8 93 EboΔ3 1.7 8 5.3 95 EboΔ4 3 12 4.1 62

Vector was administered intramuscularly (10¹¹ genome copies/cell) inC57BL/6 mice and the presence of virus neutralizing antibody (VNA0 wasevaluated 28 days later as a first measure of an immune responsegenerated against the Ebola envelope glycoprotein. VNA is defined hereas serum antibody able to inhibit transduction of HeLa cells mediated byHIV-based vector pseudotyped with the wild-type Ebola envelope.

VNA to the EboZ pseudotypes was detected with AdPan7 (C7) yieldinghigher titers than AdHu5. The EboZΔ3 elicited the highest VNA in termsof the transgene targets. For the data summarized in the followingtable, neutralizing antibody titers to HIV-EboZ-GFP pseudotypes(reciprocal dilution) are provided (N=5 animals/group).

VNA Titers EboZ wildtype EboZs EboZΔ3 AdHu5 12 16 12 AdC7 44 12 140

Example 14 Pan7-Mediated Expression of Ebola Proteins

Mouse studies to evaluate Pan-7 vectors expressing Ebola envelopeproteins and the Ebola nuclear antigen have been initiated. These aredirected towards evaluation of neutralizing antibodies in C57Bl/6 miceinjected intramuscularly (IM) with Adhu5 or Pan-7 expressing each of 4Ebola env constructs.

A. Evaluation of CTL from C57Bl/6 Mice Injected IM with Adhu5 or Pan-7Expressing the Ebola Env Constructs.

1. Challenge Experiment in Mice with Ebola Virus.

Neutralizing antibody (NAB) responses to the Ebola envelope wereanalyzed by looking at immunized mouse sera mediated neutralization of alentiviral (HIV) vector pseudotyped with the several constructs (eEbo,NTD2, NTD3, NTD4) of the Ebola envelope glycoprotein. C57BL/6 or BALB/cmice received a single intramuscular injection of 5×10¹⁰ particles permouse of C7 (Ad Pan-7) encoding Ebola envelope variant. Neutralizingantibody was evaluated 30 days post-vaccination. Briefly, Ebola Zairepseudotyped HIV vector encoding for β-galactosidase (EboZ-HIV-LacZ) wasincubated for 2 hr at 37° C. with different dilution of heat inactivatedmouse serum. Following the incubation with serum, EboZ-HIV-LacZ was thenused to infect HeLa cells for 16 hr at 37° C. Infectivity was revealedby X-gal staining of transduced HeLa cells positive for β-galactosidase.Neutralizing titer represent the serum reciprocal dilution where a 50%decrease in the number of β-galactosidase positive blue cells wasobserved. Sera were collected 30 days post-immunization, which consistedin a single intramuscular (I.M.) administration of 5×10¹⁰particles/animal. Neutralizing antibody to Ebola pseudotyped HIV couldbe detected from all groups with antibody titers ranging from 20 forAd-EboZ (Adhu5 expressing EboZ), Ad-NTD3 (Adhu5 expressing NTD3) andC7-sEbo (Ad Pan-7 expressing soluble EboZ) to over 130 for C7-NTD3 (AdPan-7 expressing soluble NTD3) and C7-NTD4 (Ad Pan-7 expressing solubleNTD3). The same immunization strategy in BALB/c mice resulted in lowerneutralizing antibody titers for Ad- and C7-NTD2, and NTD4.

B. Cellular Immune Response

The cellular immune response to the Ebola envelope in C57BL/6 mice wasevaluated 8 days after a single I.M. administration of 5×10¹⁰ particlesof C7-LacZ or C7-Ebola envelope variant per animal. Mice were vaccinatedI.M. with 5×10¹⁰ particles of C7 encoding LacZ or Ebola envelopevariant. Splenic lymphocytes from immunized mice were collected 8 dayspost vaccination and stimulated in vitro with feeder cells (spleniclymphocytes from untreated mice infected with human Adenovirus serotype5 encoding for the wild-type Ebola envelope and irradiated). Standard5-hr CTL assays were performed using ⁵¹Cr-labeled syngenic C57 cellstransfected with an expresser of EboZ.

A positive MHC-restricted cytotoxic T lymphocyte (CTL) response wasobserved from all AdPan-7 encoding for Ebola envelope variants with ahigher response from NTD2, NTD3 or NTD4 immunized mice. Indeed, effectorcells from C7 encoding Ebola envelope variant immunized mice recognizedEboZ transfected target cells and gave recall CTL responses up to 30%specific lysis. Less than 5% lysis was seen with effector cells fromnaïve or LacZ immunized control mice confirming that lysis was specificfor Ebola envelope antigens.

C. Protection Studies

The most direct means of evaluating C7 (Ad Pan-7) encoding for the EboZvariants as a successful vaccine in mice was to assess protectionagainst weight loss and death following lethal challenge with mouseadapted Ebola Zaire virus. BALB/c mice were immunized with a single doseof 5×10¹⁰ particles per animal as performed previously and vaccinatedanimals were challenged with 200 LD₅₀ of mouse adapted Ebola Zaire 21days later. All control mice (vehicle and C7-LacZ) died between day 5 today 9 post-challenge. In contrast, all vaccinated mice but one, (fromthe C7-sEbo group), survived the challenge with Ebola Zaire.

Weight loss was observed from mice vaccinated with C7-sEbo from day 4 today 7. Signs of illness such as pilo-erection and from light to severelethargy were also noted from mice vaccinated with C7-sEbo, NTD2 andNTD3 between day 4 to day 7. Mice immunized with C7-EboZ and C7-NTD4 didnot show sign of illness. Overall, a single dose of C7-EboZ and C7-NTD4completely protected immunized mice from illness and death possibly dueto a significant T cell mediated immunity.

All documents recited above are incorporated herein by reference, as arepriority applications, U.S. patent application Ser. No. 14/073,979,filed Nov. 7, 2013, U.S. patent application Ser. No. 13/337,608, filedDec. 27, 2011, U.S. patent application Ser. No. 11/820,439, filed Jun.19, 2007, now U.S. Pat. No. 8,105,574, U.S. patent application Ser. No.10/494,364, filed May 12, 2004, now U.S. Pat. No. 7,247,472, issued Jul.24, 2007, which is a 371 of PCT/US 02/33645, filed Nov. 20, 2002, whichclaims the benefit under 35 USC 119(e) of U.S. Provisional PatentApplication No. 60/366,798, filed Mar. 22, 2002 and U.S. ProvisionalPatent Application No. 60/331,951, filed Nov. 21, 2001, now expired.Numerous modifications and variations of the present invention areincluded in the scope of the above-identified specification and areexpected to be obvious to one of skill in the art. Such modificationsand alterations to the compositions and processes of the presentinvention, such as selections of different minigenes or selection ordosage of the vectors or immune modulators are believed to be within thescope of the claims appended hereto.

What is claimed is:
 1. A recombinant adenovirus having a capsidcomprising a SV39 hexon protein having the amino acid sequence of SEQ IDNO: 36, having packaged therein a nucleic acid sequence comprising (a)an adenovirus 5′ inverted terminal repeat sequence, (b) a nucleotidesequence heterologous to SV39 encoding a therapeutic or immunogenicproduct operably linked to expression control sequences which directtranscription, translation, and/or expression thereof in a host cell,and (c) an adenovirus 3′ inverted terminal repeat sequence.
 2. Therecombinant adenovirus according to claim 1, wherein the capsid furthercomprises a SV39 fiber protein.
 3. The recombinant adenovirus accordingto claim 2, wherein the adenovirus fiber protein has the sequence of SEQID NO:
 37. 4. The recombinant adenovirus according to claim 1, whereinthe capsid further comprises a SV39 penton protein.
 5. The recombinantadenovirus according to claim 4, wherein the adenovirus fiber proteinhas the sequence of SEQ ID NO:
 35. 6. The recombinant adenovirusaccording to claim 1, wherein the adenovirus further comprises anadenovirus capsid protein heterologous to SV39.
 7. The recombinantadenovirus according to claim 1, wherein the recombinant adenovirus is apseudotyped adenovirus comprising 5′ and 3′ adenovirus cis-elementsnecessary for replication and encapsidation, said cis-elementscomprising an adenovirus 5′ inverted terminal repeat and an adenovirus3′ inverted terminal repeat which are heterologous to SV39.
 8. Therecombinant adenovirus according to claim 1, wherein said adenoviruscomprises minimal genomic adenovirus sequences which lacks all or a partof the E1 gene.
 9. The recombinant adenovirus according to claim 1,wherein the heterologous adenovirus capsid protein is selected from oneor more of (a) a penton protein, (b) a fiber protein. (c) a protein ofthe adenovirus L1 region selected from the 28.1 kD protein, polymerase,agnoprotein, 52/55 kD protein, and/or IIIa protein; (d) a protein of theadenovirus L2 region selected from the VII, VI, and/or Mu proteins; (e)a protein of the adenovirus L3 region selected from the VI and/orendoprotease; and (f) a protein of the adenovirus L4 region selectedfrom the 100 kD protein, the 33 kD homolog, and/or VIII.
 10. Acomposition comprising the recombinant adenovirus according to claim 1and a pharmaceutically acceptable carrier, adjuvant, stabilizer, and/orpreservative.
 11. A synthetic simian adenovirus serotype nucleic acidsequence selected from one or more of the group consisting of: (a) 5′inverted terminal repeat (ITR) sequences; (b) the adenovirus E1a region,or a fragment thereof selected from among the 13S, 12S and 9S regions;(c) the adenovirus E1b region, or a fragment thereof selected from amongthe group consisting of the small T, large T, IX, and IVa2 regions; (d)the E2b region; (e) the L1 region, or a fragment thereof selected fromamong the group consisting of the 28.1 kD protein, polymerase,agnoprotein, 52/55 kD protein, and IIIa protein; (f) the L2 region, or afragment thereof selected from the group consisting of the penton, VII,VI, and Mu proteins; (g) the L3 region, or a fragment thereof selectedfrom the group consisting of the VI, hexon, or endoprotease; (h) the 2aprotein; (i) the L4 region, or a fragment thereof selected from thegroup consisting of the 100 kD protein, the 33 kD homolog, and VIII; (j)the E3 region, or a fragment thereof selected from the group consistingof E3 ORF1, E3 ORF2, E3 ORF3, E3 ORF4, E3 ORF5, E3 ORF6, E3 ORF7, E3ORF8, and E3 ORF9; (k) the L5 region, or a fragment thereof selectedfrom a fiber protein; (l) the E4 region, or a fragment thereof selectedfrom the group consisting of E4 ORF7, E4 ORF6, E4 ORF4, E4 ORF3, E4ORF2, and E4 ORF1; and (m) the 3′ ITR, of any of Pan5 SEQ ID NO:1; SV1SEQ ID NO: 24; SV25 SEQ ID NO: 29; and SV39 SEQ ID NO: 34, or sequencecomplementary to any of (a) to (m).
 12. A recombinant nucleic acidmolecule comprising a heterologous simian adenoviral sequence accordingto claim
 11. 13. The nucleic acid molecule according to claim 12,wherein said simian adenoviral sequence encodes an adenoviral geneproduct and is operatively linked to regulatory control sequences whichdirect expression of the adenoviral gene product in a host cells.
 14. Amethod for targeting a cell having an adenoviral receptor comprisingdelivering to a subject a recombinant adenovirus according to claim 1.15. A recombinant vector comprising a nucleic acid molecule according toclaim 12 and a heterologous gene operatively linked to sequences whichdirect expression of said gene in a host cell.
 16. The recombinantvector according to claim 15, further comprising 5′ and 3′ adenoviruscis-elements necessary for replication and encapsidation.
 17. Therecombinant vector according to claim 15, wherein said vector is anadenovirus.
 18. The recombinant vector according to any of claim 17,wherein said adenovirus lacks all or a part of the E1 gene.
 19. A methodfor delivering a heterologous gene to a mammalian cell comprisingintroducing into said cell an effective amount of an adenovirusaccording to claim
 17. 20. A method for targeting a cell having anadenoviral receptor comprising delivering to a subject a recombinantadenovirus according to claim 17.